diff --git a/articles/pedsuite.html b/articles/pedsuite.html index 0a7ee65..15fd267 100644 --- a/articles/pedsuite.html +++ b/articles/pedsuite.html @@ -174,7 +174,7 @@

3. Realised inbreeding (ibdsim2#> Recomb model : chi #> Target indivs: 1-9 #> Skip recomb : - -#> Total time used: 1.81 secs +#> Total time used: 1.82 secs

Now extract the autozygous segments of each simulation.

 fr = realisedInbreeding(sims, id = 9)
diff --git a/articles/web_only/course-ghep2024.html b/articles/web_only/course-ghep2024.html index 1e7638b..4c23653 100644 --- a/articles/web_only/course-ghep2024.html +++ b/articles/web_only/course-ghep2024.html @@ -156,7 +156,7 @@

Oct 21: Relatedness inferenceRealised relatedness: Why are some siblings more alike than others? (MDV) -
  • 17:00–17:45 Exercises V. (Solutions)
    • +
  • 17:00–17:45 Exercises V. (Solutions)
  • 17:45–18:00 Break
  • 18:00–19:00 Pedigree reconstruction (MDV)
    • diff --git a/pkgdown.yml b/pkgdown.yml index 8405d72..2ef8e19 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -17,7 +17,7 @@ articles: pedsuite: pedsuite.html web_only/publications: web_only/publications.html web_only/quickped: web_only/quickped.html -last_built: 2024-10-21T16:01Z +last_built: 2024-10-21T17:00Z urls: reference: https://magnusdv.github.io/pedsuite/reference article: https://magnusdv.github.io/pedsuite/articles diff --git a/search.json b/search.json index 566152d..22e5144 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://magnusdv.github.io/pedsuite/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://magnusdv.github.io/pedsuite/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started with the pedsuite","text":"following command installs latest official versions pedsuite packages: Alternatively, can install development versions GitHub: need packages, may choose install individually instead entire collection.","code":"install.packages(\"pedsuite\") # install.packages(\"devtools\") devtools::install_github(\"magnusdv/pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"a-quick-tour","dir":"Articles","previous_headings":"","what":"A quick tour","title":"Getting started with the pedsuite","text":"aim vignette illustrate possibilities pedsuite packages. noted barely scratching surface ; particular several packages even mentioned. comprehensive overview, recommend book. get started load pedsuite package, convenient shortcut loading core packages, making methods available current R session.","code":"library(pedsuite) #> Loading required package: forrel #> Loading required package: pedtools #> Loading required package: pedprobr #> Loading required package: ribd #> Loading required package: verbalisr"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"create-a-pedigree-pedtools","dir":"Articles","previous_headings":"A quick tour","what":"1. Create a pedigree (pedtools)","title":"Getting started with the pedsuite","text":"begin creating plotting pedigree child first cousins: symmetry let us change sex individual 3. also take opportunity showcase plot options (many available - see help page typing ?plotmethods):","code":"x = cousinPed(1, child = TRUE) plot(x) x = swapSex(x, ids = 3) #> Changing sex of spouses as well: 4 plot(x, hatched = 9, carrier = 7:8, fill = list(pink = 1), textAnnot = list(inside = c(\"1\" = \"?\")))"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"calculate-the-inbreeding-coefficient-ribd","dir":"Articles","previous_headings":"A quick tour","what":"2. Calculate the inbreeding coefficient (ribd)","title":"Getting started with the pedsuite","text":"inbreeding coefficient ff pedigree member defined probability autozygosity random autosomal locus. , probability two homologous alleles origin within pedigree. child first cousins one can work pen paper f=1/16f = 1/16. Alternatively, can calculate ribd function inbreeding(). output agrees f=1/16f = 1/16.","code":"inbreeding(x, ids = 9) #> [1] 0.0625"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"realised-inbreeding-ibdsim2","dir":"Articles","previous_headings":"A quick tour","what":"3. Realised inbreeding (ibdsim2)","title":"Getting started with the pedsuite","text":"particular child first cousins, actual autozygous fraction genome (except X & Y) called coefficient realised inbreeding, denoted fRf_R. may deviate substantially pedigree-based expectation f=1/16f = 1/16. can simulate distribution fRf_R ibdsim2 package. Since core package must load separately. First, use function ibdsim() simulate recombination process entire pedigree, 200 times: Now extract autozygous segments simulation. summary first 6 simulations, including number segments various length statistics: histogram realised inbreeding coefficients (given right-column ): see, distribution centres around expectation f=1/16=0.0625f = 1/16 = 0.0625 (red vertical line) substantial spread. sample standard deviation can found fr$stDev, case 0.02.","code":"library(ibdsim2) sims = ibdsim(x, N = 200, seed = 123) #> Simulation parameters: #> Simulations : 200 #> Chromosomes : 1-22 #> Genome length: 2753.93 Mb #> 2602.29 cM (male) #> 4180.42 cM (female) #> Recomb model : chi #> Target indivs: 1-9 #> Skip recomb : - #> Total time used: 1.81 secs fr = realisedInbreeding(sims, id = 9) head(fr$perSimulation) #> nSeg meanLen totLen maxLen minLen fReal #> 1 11 19.05892 209.6481 37.60149 0.8069583 0.06181840 #> 2 12 14.17339 170.0807 48.43095 1.3405519 0.05015126 #> 3 12 12.87321 154.4785 26.10949 0.1452881 0.04555068 #> 4 19 17.44059 331.3712 58.63821 1.2124618 0.09771059 #> 5 16 16.95554 271.2886 44.95560 1.0034634 0.07999419 #> 6 13 17.84055 231.9271 49.91405 0.9327245 0.06838775 hist(fr$perSimulation$fReal, xlim = c(0, 0.15), breaks = 16, xlab = \"f_R\", main = NULL) # Expected value abline(v = 1/16, col = 2)"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"marker-simulation-forrel","dir":"Articles","previous_headings":"A quick tour","what":"4. Marker simulation (forrel)","title":"Getting started with the pedsuite","text":"Note everything done far purely theoretical, markers involved. medical forensic applications usually work genetic data form marker genotypes, let us simulate dataset family. markerSim() function forrel package simulates genotypes pedigree members specific type markers. instance, produce 500 SNPs alleles B (equally frequent, default): can see genotypes first markers printing y console.","code":"y = markerSim(x, N = 500, alleles = c(\"A\", \"B\")) #> Unconditional simulation of 500 autosomal markers. #> Individuals: 1, 2, 3, 4, 5, 6, 7, 8, 9 #> Allele frequencies: #> A B #> 0.5 0.5 #> Mutation model: No #> #> Simulation finished. #> Calls to `likelihood()`: 0. #> Total time used: 0 seconds. y #> id fid mid sex <1> <2> <3> <4> <5> #> 1 * * 1 A/B B/B A/A B/B A/A #> 2 * * 2 A/B A/B A/B A/A A/B #> 3 1 2 2 A/B A/B A/B A/B A/B #> 4 * * 1 A/B A/B B/B A/B A/B #> 5 1 2 1 B/B A/B A/B A/B A/A #> 6 * * 2 A/B B/B A/A A/B A/A #> 7 4 3 1 B/B A/A B/B A/B A/B #> 8 5 6 2 A/B A/B A/B B/B A/A #> 9 7 8 1 B/B A/A B/B B/B A/A #> Only 5 (out of 500) markers are shown."},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"inference-of-pairwise-relationships-forrel","dir":"Articles","previous_headings":"A quick tour","what":"5. Inference of pairwise relationships (forrel)","title":"Getting started with the pedsuite","text":"real dataset, natural quality control step check correctness pedigree. One way use data estimate pairwise relationship, compare result pedigree. function checkPairwise() , presents result relationship triangle. plot shows pairwise estimates near expected location triangle.","code":"checkPairwise(y) #> Excluding inbred individuals: 9"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"where-to-go-from-here","dir":"Articles","previous_headings":"","what":"Where to go from here","title":"Getting started with the pedsuite","text":"enjoyed quick tour like details, check GitHub README files packages interest , instance: pedtools: Creating working pedigrees marker data forrel: Forensic pedigree analysis relatedness analysis ribd: Computation pedigree-based relatedness coefficients verbalisr: Verbal descriptions pedigree relationships ibdsim2: Simulation identity--descent sharing family members dvir: Disaster victim identification Try interactive pedigree builder QuickPed: https://magnusdv.shinyapps.io/quickped. pedtools vignette contains details pedigree objects R plot manipulate .","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"learning-outcomes","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcomes","title":"GHEP Online School 2024: Workshop 1","text":"Classical concepts methods genetic relatedness Using QuickPed apps pedigree analysis Using Familias software perform kinship testing Methods relationship inference pedigree reconstruction Practical methods disaster victim identification","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"software-preparation-r","dir":"Articles > Web_only","previous_headings":"","what":"Software preparation: R","title":"GHEP Online School 2024: Workshop 1","text":"Several exercises use R. order , please install following computer: recent version R RStudio Run following command R install pedsuite packages:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"software-preparation-familias","dir":"Articles > Web_only","previous_headings":"","what":"Software preparation: Familias","title":"GHEP Online School 2024: Workshop 1","text":"Part course based kinship testing Familias software, can installed : https://familias./download.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"GHEP Online School 2024: Workshop 1","text":"course runs Monday October 2024, 16 20 (CEST). following schedule tentative:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-7-theory-of-relatedness","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 7: Theory of relatedness","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 Introduction pedigrees, QuickPed R (MDV) 17:00–17:45 Exercises . (Solutions) 17:45–18:00 Break 18:00–19:00 Measures relatedness (MDV) 19:00–19:45 Exercises II. (Solutions) 19:45–20:00 Wrap-","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-14-kinship-testing","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 14: Kinship testing","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 Introduction forensic kinship testing (TE) 17:00–17:45 Exercises III. (Solutions) 17:45–18:00 Break 18:00–19:00 Kinship testing Familias (TE) 19:00–19:45 Exercises IV. File needed: kinship-riddle.fam. (Solutions) 19:45–20:00 Wrap-","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-21-relatedness-inference","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 21: Relatedness inference","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 Realised relatedness: siblings alike others? (MDV) 17:00–17:45 Exercises V. (Solutions) 17:45–18:00 Break 18:00–19:00 Pedigree reconstruction (MDV) 19:00–19:45 Exercises VI 19:45–20:00 Wrap-","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-28-disaster-victim-identification","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 28: Disaster victim identification","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 DNA-based disaster victim identification (TE) 17:00–17:45 Exercises VII 17:45–18:00 Break 18:00–19:00 Practical DVI Diviana (MDV) 19:00–19:45 Exercises VIII 19:45–20:00 Wrap-Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"description","dir":"Articles > Web_only","previous_headings":"","what":"Description","title":"ISFG Summer School - Virtual Edition 2021","text":"study genetic relatedness genetic information flows families, central variety research fields, including medical forensic genetics. aim course introduce elegant statistical foundations relatedness, well several forensic applications, particular focus using R calculations visualisations. lectures exercises based book Pedigree Analysis R. 30% discount available participants (buy book order attend course).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcome","title":"ISFG Summer School - Virtual Edition 2021","text":"completing course participants knowledge : Classical concepts methods statistical genetics relatedness analysis create, manipulate plot pedigrees R compute pedigree likelihoods likelihood ratios R perform kinship testing pedigree reconstruction R perform disaster victim identification R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"","what":"Prerequisites","title":"ISFG Summer School - Virtual Edition 2021","text":"Basic knowledge genetics probability. previous experience R recommended. Please make sure R (version > 4.0) installed computer. recommend running R RStudio. following R command installs pedsuite packages, used throughout course:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"ISFG Summer School - Virtual Edition 2021","text":"course runs 14 18 (CEST) day, 15 minute break middle. lectures aimed 55 minutes, allowing short interval exercises.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"day-1-july-28-wednesday","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Day 1 — July 28 (Wednesday)","title":"ISFG Summer School - Virtual Edition 2021","text":"14:00–15:00 Lecture 1. Introductions (MDV) 15:00–15:45 Exercise set 1 15:45–16:00 Break 16:00–17:00 Lecture 2. Working pedigrees R (MDV) 17:00–18:00 Exercise set 2","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"day-2-july-29-thursday","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Day 2 — July 29 (Thursday)","title":"ISFG Summer School - Virtual Edition 2021","text":"14:00–15:00 Lecture 3. Kinship testing: paternity cases complex cases (TE) 15:00–15:45 Exercise set 3 15:45–16:00 Break 16:00–17:00 Lecture 4. Relatedness coefficients (MDV) 17:00–18:00 Exercise set 4","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"day-3-july-30-friday","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Day 3 — July 30 (Friday)","title":"ISFG Summer School - Virtual Edition 2021","text":"14:00–15:00 Lecture 5. Relatedness inference pedigree reconstruction (MDV) 15:00–15:45 Exercise set 5 15:45–16:00 Break 16:00–17:00 Lecture 6. Disaster victim identification forensic applications (TE) 17:00–18:00 Exercise set 6 Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"description","dir":"Articles > Web_only","previous_headings":"","what":"Description","title":"ISFG Summer School 2023","text":"study genetic relatedness flow genetic information within families, central forensic genetics. aim course introduce elegant statistical foundations relatedness, explore important forensic applications. use software R calculations visualisations, particular pedsuite packages pedigree analysis. lectures exercises based book Pedigree Analysis R (need book order attend course).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcome","title":"ISFG Summer School 2023","text":"completing course participants knowledge : Classical concepts statistical genetics relatedness analysis produce informative beautiful pedigree plots compute coefficients relatedness perform kinship testing pedigree reconstruction R perform disaster victim identification R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"","what":"Prerequisites","title":"ISFG Summer School 2023","text":"Basic knowledge genetics probability previous experience R recommended, strictly required recent version R (least 4.1) must installed computer recommend running R RStudio following R command installs pedsuite packages, used throughout course:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"ISFG Summer School 2023","text":"course runs 18 22 (CEST) day, 15 minute break middle. following schedule tentative:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"aug-30-wednesday-pedigree-analysis-basic","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Aug 30 (Wednesday) – Pedigree analysis: Basic","title":"ISFG Summer School 2023","text":"18:00–19:00 Pedigrees measures relatedness (MDV) 19:00–19:15 Crash course R (MDV) 19:15–20:00 Exercises 20:00–20:15 Break 20:15–21:00 Kinship testing (TE) 21:00–21:45 Exercises II 21:45–22:00 Summary discussion","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"aug-31-thursday-pedigree-analysis-advanced","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Aug 31 (Thursday) – Pedigree analysis: Advanced","title":"ISFG Summer School 2023","text":"18:00–19:00 Relatedness inference pedigree reconstruction (MDV) 19:00–19:45 Exercises III 19:45–20:00 Break 20:00–21:00 Disaster victim identification (TE) 21:00–21:45 Exercises IV 21:45–22:00 Summary discussion Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"kinship-statistics-and-pedigree-analysis","dir":"Articles > Web_only","previous_headings":"","what":"Kinship Statistics and Pedigree Analysis","title":"ISFG Congress 2024 Workshop","text":"Date: Tuesday, 10th September, 2024 : San Francisco Hotel Monumento, Santiago de Compostela, Spain Teachers: Magnus Dehli Vigeland Thore Egeland ISFG 2024 workshops: https://isfg2024.com/pre-congress-workshops/","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"description","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Description","title":"ISFG Congress 2024 Workshop","text":"study pedigrees genetic relatedness central forensic genetics. aim course introduce elegant statistical foundations relatedness, well several forensic applications. certain parts use R calculations visualisations. basic session focus pedigree coefficients likelihood ratios kinship analysis. addition, demonstrate QuickPed, online tool creating pedigrees computing relatedness: https://magnusdv.shinyapps.io/quickped advanced part explore recently developed methods implementations Disaster Victim Identification (DVI) pedigree reconstruction. course material based book Pedigree Analysis R (Vigeland ’21) selected papers. session alternate lectures hands-exercises. Solutions exercises provided discussed end session. Attendance ‘Basic session’ required ‘Advanced session’ participants familiar R.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Learning outcome","title":"ISFG Congress 2024 Workshop","text":"completing course participants knowledge : Classical concepts statistical genetics relatedness analysis produce informative beautiful pedigree plots compute coefficients relatedness perform kinship testing pedigree reconstruction R perform disaster victim identification R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Prerequisites","title":"ISFG Congress 2024 Workshop","text":"Basic knowledge genetics probability participants must bring laptop administrative rights recent version R (least 4.1) must installed computer previous experience R recommended, strictly required strongly recommend running R RStudio","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Schedule","title":"ISFG Congress 2024 Workshop","text":"workshop run full-day course Tuesday 10th, 9 18:30 (CEST). following schedule tentative:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"morning-session-pedigree-analysis-basic","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis > Schedule","what":"Morning session – Pedigree analysis: Basic","title":"ISFG Congress 2024 Workshop","text":"09:00–10:00 Pedigrees measures relatedness (MDV) 10:00–11:00 Exercises 11:00–11:15 Break 11:15–12:00 Kinship testing (TE) 12:00–12:45 Exercises II 12:45–13:00 Summary discussion Lunch break 13:00 - 14:30","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"afternoon-session-pedigree-analysis-advanced","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis > Schedule","what":"Afternoon session – Pedigree analysis: Advanced","title":"ISFG Congress 2024 Workshop","text":"14:30–15:30 Relatedness inference pedigree reconstruction (MDV) 15:30–16:15 Exercises III 16:15–16:30 Break 16:30–17:30 Disaster victim identification (TE) 17:30–18:15 Exercises IV 18:15–18:30 Summary discussion Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"summary","dir":"Articles > Web_only","previous_headings":"","what":"Summary","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"Title: Statistical methods relatedness pedigree analysis Dates: 13–17 June 2022 Teachers: Magnus Dehli Vigeland Thore Egeland : Room 2203a (“Helix”), Kristine Bonnevies hus, University Oslo Address: Blindernveien 31, entrance Moltke Moes vei. Credits: 4 ECTS Exam: Home project (passed/passed)","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"description","dir":"Articles > Web_only","previous_headings":"","what":"Description","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"course introduces statistical methods used relatedness pedigree analysis, applications forensic genetics, medical genetics pedigree reconstruction. study genetic relatedness genetic information flows families, central variety important research fields, including medical genetics, forensics animal breeding. aim course introduce students elegant concepts results forming theoretical foundation genetic relatedness, present detail several modern applications. exercises use R pedsuite packages pedigree analysis visualisation. Much course material based book Pedigree Analysis R may interest participants (required attend course).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcome","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"completing course participants knowledge : Classical concepts methods statistical genetics relatedness analysis Important applications pedigree analysis, including forensic kinship analysis, medical segregation analysis pedigree reconstruction work pedigrees R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"","what":"Prerequisites","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"Basic knowledge genetics probability. previous experience R recommended, strictly required. Please make sure R (version > 4.1) installed computer. strongly recommend running R RStudio. following R command installs pedsuite packages, used throughout course:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"course runs 9 16.30 (CEST) day. tentative schedule given . Minor changes may occur.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"monday-june-13","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Monday, June 13","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Introduction : Pedigrees, genetics probabilities (MDV) 11–12 Exercises 12–13 Lunch 13–15 Introduction II: R pedsuite (MDV) 15–16:30 Exercises II","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"tuesday-june-14","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Tuesday, June 14","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Relatedness : IBD coefficients relatedness (MDV) 11–12 Exercises III 12–13 Lunch 13–15 Relatedness II: Realised relatedness (MDV) 15–16:30 Exercises IV","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"wednesday-june-15","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Wednesday, June 15","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Forensic applications (TE) 11–12 Exercises V 12–13 Lunch 13–15 Inference relatedness pedigree reconstruction (MDV) 15–16:30 Exercises VI","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"thursday-june-16","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Thursday, June 16","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Forensic applications II (TE) 11–12 Exercises VII 12–13 Lunch 13–15 Linkage segregation analysis medical genetics (MDV) 15–16:30 Exercises VIII","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"friday-june-17","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Friday, June 17","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Genealogical triangulation (TE/MDV) 11–12 Exercises 12–13 Lunch 13–16:30 Case study wrap (MDV) Comments questions may sent magnusdv medisin uio .","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"workshop-genetic-relatedness","dir":"Articles > Web_only","previous_headings":"","what":"Workshop: Genetic relatedness","title":"Young Investigator Day 2024","text":"Date: Monday 14th October, 2024 : Cancer Registry Norway Teacher: Magnus Dehli Vigeland Part NOFE conference (Norwegian Epidemiological Association)","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"description","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Description","title":"Young Investigator Day 2024","text":"study pedigrees genetic relatedness central many fields, including medical genetics, forensics epidemiology. aim course introduce elegant statistical foundations relatedness, well relevant software tools. workshop alternate lectures hands-exercises. exercises use R, others use QuickPed, free online tool creating analysing pedigrees: https://magnusdv.shinyapps.io/quickped course material based book Pedigree Analysis R (Vigeland ’21), may point reference participants want delve deeper subject.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Learning outcome","title":"Young Investigator Day 2024","text":"completing course participants knowledge : Classical concepts statistical genetics relatedness analysis produce informative beautiful pedigree plots compute coefficients relatedness siblings related others","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Prerequisites","title":"Young Investigator Day 2024","text":"Basic knowledge genetics probability participants must bring laptop recent version R installed (least 4.3.0) strongly recommend running R RStudio","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Schedule","title":"Young Investigator Day 2024","text":"workshop run half-day course, 12 16, following (tentative) schedule: 12:00–13:00 Introduction pedigrees relationships 13:00–13:45 Exercises . (Solutions) 13:45–14:00 Break 14:00–15:00 Measures relatedness 15:00–15:45 Exercises II. (Solutions) 15:45–16:00 Summary discussion Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"upcoming-events","dir":"Articles > Web_only","previous_headings":"","what":"Upcoming events","title":"Talks and courses based on the pedsuite","text":"Oct 7,14,21 28, 2024. Kinship pedigree analysis: Methods applications. Four-part lecture series, part ISFG-GHEP Online School 2024. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage.","code":""},{"path":[]},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section","dir":"Articles > Web_only","previous_headings":"Past events","what":"2024","title":"Talks and courses based on the pedsuite","text":"Oct 15. DIVIANA: free, user-friendly app complex DVI cases. Research seminar RMF, Storo, Oslo. Speaker: Magnus D. Vigeland. Oct 14. Genetic Relatedness. Half-day workshop Young Investigator Day NOFE Conference. Lecturer: Magnus D. Vigeland. Course homepage. Oct 10. DIVIANA: free, user-friendly app complex DVI cases. Invited online talk 2nd Intl Symposium DNA Supported Missing Persons Disaster Victim Identification, Tbilisi, Georgia. Speaker: Magnus D. Vigeland. Slides (extended version ISFG talk). Sept 24. Advanced Theoretical Challenges: Kinship. Presentation solutions results theoretical proficiency test prepared ISFG-GHEP 2024. Exercises. Presentation. Sept 11. DIVIANA: free, user-friendly app complex DVI cases. Oral presentation ISFG Congress 2024, Santiago de Compostela. Speaker: Magnus D. Vigeland. Slides. Sept 10. Kinship statistics pedigree analysis. Pre-congress workshop, ISFG Congress 2024, Santiago de Compostela. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-1","dir":"Articles > Web_only","previous_headings":"Past events","what":"2023","title":"Talks and courses based on the pedsuite","text":"Aug 30-31. Pedigree Analysis. ISFG Summer School 2023. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-2","dir":"Articles > Web_only","previous_headings":"Past events","what":"2022","title":"Talks and courses based on the pedsuite","text":"June 13-17. Statistical methods relatedness pedigree analysis. NORBIS 1-week intensive course, Oslo, Norway. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage. Lecture: Pedigrees relatedness analysis R Lecture: Introduction pedsuite Exercises 1: Pedigree analysis R Exercises 2: Forensic case studies","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-3","dir":"Articles > Web_only","previous_headings":"Past events","what":"2021","title":"Talks and courses based on the pedsuite","text":"Lecture 1: enough data? Lecture 2: exhumed? Jul 28-30. Pedigree Analysis R. ISFG Summer School - Virtual Edition 2021. Teachers: Thore Egeland Magnus D. Vigeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-4","dir":"Articles > Web_only","previous_headings":"Past events","what":"2020","title":"Talks and courses based on the pedsuite","text":"Jan 06-10. Statistical methods relatedness pedigree analysis. NORBIS 1-week intensive course, Oslo, Norway. Teachers: Thore Egeland Magnus D. Vigeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-5","dir":"Articles > Web_only","previous_headings":"Past events","what":"2018","title":"Talks and courses based on the pedsuite","text":"Jan 08-12. Statistical methods relatedness pedigree analysis. NORBIS 1-week intensive course, Oslo, Norway. Teachers: Thore Egeland Magnus D. Vigeland. Details program.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-6","dir":"Articles > Web_only","previous_headings":"Past events","what":"2016","title":"Talks and courses based on the pedsuite","text":"Nov 16-19. Statistical methods genetics using R. 4-day intensive course, Rio de Janeiro, Brazil. Teachers: Thore Egeland Magnus D. Vigeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/diviana.html","id":"what-is-diviana","dir":"Articles > Web_only","previous_headings":"","what":"What is DIVIANA?","title":"DIVIANA","text":"DIVIANA user-friendly app disaster victim identification (DVI).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/ibdClassifier.html","id":"what-is-ibdclassifier","dir":"Articles > Web_only","previous_headings":"","what":"What is ibdClassifier?","title":"ibdClassifier","text":"ibdClassifier tool predicting pairwise relationship based set IBD segments. implements Bayes classifier using number segments lengths.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/ibdClassifier.html","id":"note-still-under-development","dir":"Articles > Web_only","previous_headings":"What is ibdClassifier?","what":"Note: Still under development","title":"ibdClassifier","text":"ibdClassifier experimental app currently development. yet ready used critical real-world applications.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/ibdsim2shiny.html","id":"what-is-ibdsim2-shiny","dir":"Articles > Web_only","previous_headings":"","what":"What is ibdsim2-shiny?","title":"ibdsim2-shiny","text":"online tool visualising comparing distributions IBD-sharing pedigree members.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/klink.html","id":"what-is-klink","dir":"Articles > Web_only","previous_headings":"","what":"What is KLINK?","title":"KLINK - kinship with linked markers","text":"KLINK user-friendly app extending Familias software kinship calculations forensic genetics. Unlike Familias, KLINK allows pairs linked markers, often seen modern marker kits. KLINK substantial overlap Familias companion FamLink, offers several unique features: platform independent (Windows) visualisations pedigrees marker maps ready--use output reports Excel format noted KLINK currently handles pairs linked markers. general linkage, e.g. dense SNPs, recommend FamLink.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/klink.html","id":"running-klink","dir":"Articles > Web_only","previous_headings":"","what":"Running KLINK","title":"KLINK - kinship with linked markers","text":"KLINK available online app R package. latter important sensitive data want run everything locally. set , simply install CRAN can open KLINK command","code":"install.packages(\"KLINK\") KLINK::launchApp()"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/linkagelab.html","id":"what-is-linkagelab","dir":"Articles > Web_only","previous_headings":"","what":"What is LinkageLab?","title":"LinkageLab - playing with linked markers","text":"LinkageLab pedagogical tool understanding marker linkage affects likelihood ratios (LRs) kinship testing.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"book","dir":"Articles > Web_only","previous_headings":"","what":"Book","title":"Publications featuring the pedsuite","text":"book Pedigree Analysis R (Academic Press, 2021) based pedsuite contains detailed explanations examples use different packages.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"papers","dir":"Articles > Web_only","previous_headings":"","what":"Papers","title":"Publications featuring the pedsuite","text":"following list publications featuring pedsuite packages. know others, please let know!","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedsuite-multiple-packages","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedsuite (multiple packages)","title":"Publications featuring the pedsuite","text":"MD Vigeland. QuickPed: online tool drawing pedigrees analysing relatedness. BMC Bioinf, 2022. M Kruijver, J-Bright. tool simulating single source mixed DNA profiles. Forensic Sci Int: Genetics, 2022. NE Altınışık, DD Kazancı, et al. genomic snapshot demographic cultural dynamism Upper Mesopotamia Neolithic Transition. Science Advances, 2022.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"dvir","dir":"Articles > Web_only","previous_headings":"Papers","what":"dvir","title":"Publications featuring the pedsuite","text":"MD Vigeland, T Egeland. Joint DNA-based disaster victim identification. Sci Rep, 2021.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"forrel","dir":"Articles > Web_only","previous_headings":"Papers","what":"forrel","title":"Publications featuring the pedsuite","text":"FL Marsico, Caridi. Incorporating non-genetic evidence large scale missing person searches: general approach beyond filtering. Forensic Sci Int: Genetics, 2023. M Iungman, S Biagini, M Canteros et al. Empirical validation family-member prioritization approach maximize statistical power missing person cases. Forensic Sci Int: Genetics Suppl Series, 2022. Chernomoretz, F Marsico, et al. Bayesian networks DNA-based kinship analysis: Functionality validation GENis missing person identification module. Forensic Sci Int: Genetics Suppl Series, 2022. HK Brustad, M Colucci, MA Jobling NA Sheehand, T Egeland. Strategies pairwise searches forensic kinship analysis. Forensic Sci Int: Genetics, 2021. FL Marsico, MD Vigeland, T Egeland, M Herrera Piñero. Making decisions missing person identification cases low statistical power. Forensic Sci Int: Genetics, 2021. HK Brustad, MD Vigeland, T Egeland. Pairwise relatedness testing context inbreeding: expectation variance likelihood ratio. Int J Legal Med, 2020. MD Vigeland, FL Marsico, M Herrera Piñero, T Egeland. Prioritising family members genotyping missing person cases: general approach combining statistical power exclusion inclusion. Forensic Sci Int: Genetics, 2020. HK Brustad, T Egeland. impact ignoring inbreeding pairwise kinship evaluations. Forensic Sci Int: Genetics Suppl Series, 2019. MD Vigeland, T Egeland. Handling founder inbreeding forensic kinship analysis. Forensic Sci Int: Genetics Suppl Series, 2019.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"ibdsim-ibdsim2","dir":"Articles > Web_only","previous_headings":"Papers","what":"IBDsim / ibdsim2","title":"Publications featuring the pedsuite","text":"C Cavagnino, G Runfeldt, et al. Unearthing Y Harewood Cemetery inference George Washington’s Y-chromosomal haplotype. iScience, 2024. H Vinje, HK Brustad, et al. Classification breed combinations slaughter pigs based genotypes—modeling DNA samples crossbreeds fuzzy sets purebred founders. Front Genet, 2023. VM Narasimhan, R Rahbari, Scally, et al. Estimating human mutation rate autozygous segments reveals population differences human mutational processes. Nat Commun, 2017. S Steinberg, S Gudmundsdottir, G Sveinbjornsson, et al. Truncating mutations RBM12 associated psychosis. Nat Genet, 2017.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"paramlink-paramlink2","dir":"Articles > Web_only","previous_headings":"Papers","what":"paramlink / paramlink2","title":"Publications featuring the pedsuite","text":"Ø Bleka, L Prieto, P Gill. EFMrep: extension EuroForMix improved combination STR DNA mixture profiles. Forensic Sci Int: Genetics, 2022. Z Bai, N Zhang, JLiu, et al. Identification missing persons kinship analysis microhaplotype sequencing single-source DNA two-person DNA mixtures. Forensic Sci Int: Genetics, 2022. F Hendrickx, Z De Corte, G Sonet, et al. masculinizing supergene underlies exaggerated male reproductive morph spider. Nature Ecology & Evolution, 2022. W Li, X Gu, C Liu, et al. synergetic effect BARD1 mutations tumorigenesis. Nat Commun, 2021. LR Lopes, S Garcia-Hernández, M Lorenzini, et al. Alpha-protein kinase 3 (ALPK3) truncating variants cause autosomal dominant hypertrophic cardiomyopathy. Eur Heart J, 2021. AL Junior, AG González, AR Vilela, et al. Genotype-phenotype correlations hypertrophic cardiomyopathy: multicenter study Portugal Spain TPM1 p.Arg21Leu variant. Rev Esp Cardiol (English Ed), 2021. G Wu, J Ruan, J Liu, et al. Variant spectrum Formin Homology 2 Domain‐Containing 3 gene Chinese patients hypertrophic cardiomyopathy. Journal American Heart Association, 2021. SL Rydning, Dudesek, F Rimmele, et al. novel heterozygous variant ERLIN2 causes autosomal dominant pure hereditary spastic paraplegia. European journal neurology, 2018. P May, S Pichler, D Hartl, et al. Rare ABCA7 variants 2 German families Alzheimer disease. Neurology Genetics, 2018. JP Ochoa, M Sabater-Molina, JM García-Pinilla, et al. Formin homology 2 domain containing 3 (FHOD3) genetic basis hypertrophic cardiomyopathy. Journal American College Cardiology, 2018. AO Tillmar, D Kling, JM Butler, et al. DNA Commission International Society Forensic Genetics (ISFG): Guidelines use X-STRs kinship analysis. Forensic Sci Int: Genetics, 2017. IL Mero, HH Mørk, Y Sheng, et al. Homozygous KIDINS220 loss--function variants fetuses cerebral ventriculomegaly limb contractures. Human Molecular Genetics, 2017. D Kling, T Egeland, M Herrera Piñero, MD Vigeland. Evaluating statistical power DNA-based identification, exemplified ‘missing grandchildren Argentina’. Forensic Sci Int: Genetics, 2017. G Dørum, D Kling, Tillmar, MD Vigeland. Mixtures relatives linked markers. Int J Legal Med, 2016. M Szopa, AH Ludwig-Galezowska, et al. family Arg103Pro mutation NEUROD1 gene detected next-generation sequencing–clinical characteristics mutation carriers. Eur J Med Gen, 2016. T Egeland, N Pinto, MD Vigeland. general approach power calculation relationship testing. Forensic Sci Int: Genetics, 2014. T Egeland, G Dørum, MD Vigeland, NA Sheehan. Mixtures relatives: pedigree perspective. Forensic Sci Int: Genetics, 2014. G Park, J Gim, AR Kim, et al. Multiphasic analysis whole exome sequencing data identifies novel mutation ACTG1 nonsyndromic hearing loss family. BMC Genomics, 2013.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedbuildr","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedbuildr","title":"Publications featuring the pedsuite","text":"Y Wei, Q Zhu, H Wang, et al. Pairwise kinship inference pedigree reconstruction using 91 microhaplotypes. Forensic Sci Int: Genetics, 2022.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedprobr","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedprobr","title":"Publications featuring the pedsuite","text":"S Bae, S Won, H Kim. Selection evaluation bi-allelic autosomal SNP markers paternity testing Koreans. Int J Legal Med, 2021.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedtools","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedtools","title":"Publications featuring the pedsuite","text":"V Papin, G Gorjanc. Unlocking genome-based prediction selection conifers: key role within-family prediction accuracy. Preprint, 2024.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"quickped","dir":"Articles > Web_only","previous_headings":"Papers","what":"QuickPed","title":"Publications featuring the pedsuite","text":"Koch, M Slovik, et al. USP27X variants underlying X-linked intellectual disability disrupt protein function via distinct mechanisms. Life Science Alliance, 2024. R Simon, K Elísabetardóttir, G Lühke. Analysis genetic variants different horn phenotypes inheritance Icelandic sheep. Arch Anim Breed, 2024. Z Kolkova, P Durdik, et al. Identification novel RPGR mutation associated retinitis pigmentosa primary ciliary dyskinesia Slovak family: case report. Front Pediatr, 2024. TA Vaz, RM Hassunuma, et al. QUICKPED: Um breve guia de como criar rapidamente um heredograma utilizando um recurso didático -line gratuito. Rev. Multi. Educação e Meio Amb, 2024.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"ribd","dir":"Articles > Web_only","previous_headings":"Papers","what":"ribd","title":"Publications featuring the pedsuite","text":"T Nomura. Ballou’s Ancestral Inbreeding Coefficient: Formulation New Estimate Higher Reliability. Animals, 2024. MD Vigeland. Two-locus identity coefficients pedigrees. G3 Genes|Genomes|Genetics, 2023. M Kruijver, JM Curran. number alleles DNA mixtures related contributors. Forensic Sci Int: Genetics, 2022. Sharma, S Szymczak, M Rühlemann, et al. Linkage analysis identifies novel genetic modifiers microbiome traits families inflammatory bowel disease. Gut Microbes, 2022. PJ Green, J Montera. Inference complex relationships using peak height data DNA mixtures. J R Stat Soc Ser C Appl Stat, 2021. MD Vigeland. Relatedness coefficients pedigrees inbred founders. Journal Mathematical Biology, 2020.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"segregatr","dir":"Articles > Web_only","previous_headings":"Papers","what":"segregatr","title":"Publications featuring the pedsuite","text":"H-K Liu, H-L Hao, et al. Cysteinyl-tRNA Synthetase Mutation Causes Novel Autosomal-Dominant Inheritance Parkinsonism/Spinocerebellar-Ataxia Complex. Neurosci Bull, 2024. SA Schubert, D Ruano, et al. Germline variant affecting p53β isoforms predisposes familial cancer. Nat Commun, 2024. C Carrizosa, DE Undlien, MD Vigeland. shinyseg: web application flexible cosegregation sensitivity analysis. Bioinformatics, 2024. Ratajska, MD Vigeland, et al. use segregation analysis interpretation sequence variants SMAD3: case report. Molec. Genetics & Genomic Med, 2023. PM Bjørnstad, R Aaløkken, et al. 39 kb structural variant causing Lynch Syndrome detected optical genome mapping nanopore sequencing. Eur J Med Gen, 2023.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"what-is-quickped","dir":"Articles > Web_only","previous_headings":"","what":"What is QuickPed?","title":"QuickPed - a free online pedigree creator","text":"QuickPed interactive web application drawing analysing pedigrees. created pedigree may saved image text file ped format (see ). may also obtain various information pedigree, including relatedness coefficients verbal descriptions relationships. QuickPed powered pedsuite uses kinship2 alignment calculations. web app built Shiny.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"drawing-pedigrees","dir":"Articles > Web_only","previous_headings":"","what":"Drawing pedigrees","title":"QuickPed - a free online pedigree creator","text":"Creating pedigrees QuickPed intuitive: Select suitable start pedigree modify needed. may also load existing ped file (see ). Modifications done clicking one several individuals applying appropriate buttons, instance add children, siblings parents. time may change attributes like sex, affection status, twin status ID labels.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"tips-and-tricks","dir":"Articles > Web_only","previous_headings":"Drawing pedigrees","what":"Tips and tricks","title":"QuickPed - a free online pedigree creator","text":"Selecting individuals. Select/deselect pedigree members clicking . Selected individuals shown red colour. Time-saving tip: deselect everyone, click hand pointer red strikethrough. Adding parents. select single founder click “Add Parents,” new parents created individual. version 4.1.1, can also assign existing members parents. First, select child, intended parent(s) — order selection matters! Finally, click “Add Parents.” Removing individuals. removing pedigree members must decide whether want remove downwards upwards. example, pedigree , want end trio 1-2-3, select 4 /5 delete downwards ↓. Conversely, want trio 3-4-5, select 1 /2, click ↑. Note: cases, leftover founder-spouses automatically removed. Automatic labelling. Automatic labelling pedigree members available two different formats. button marked 1,2,.. applies numeric labels individuals, order appearance pedigree plot. Alternatively, -1, -2,.. button numbers members generation-wise, using Roman numerals indicate generation number. Line breaks labels. default, pedigree labels folded automatically width approximately 12 characters. insert hard line breaks, use double space. instance, want “King Lear” appear two lines, modify label “King␣␣Lear”, .e., two spaces words. Text annotation. Double clicking pedigree member opens popup window, text may added around inside symbol individual. Plot settings. pedigree gets large, increase plot region using control panel far right. may also adjust margins, size pedigree symbols text labels. R code. “R code” button, located right side QuickPed, opens text window containing R code reproduces current pedigree plot. saving .R file, simply copy-pasting code R, can explore plot options (see ?pedtools::plot.ped lots examples!) use pedigree starting point analysis pedsuite.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"built-in-pedigrees","dir":"Articles > Web_only","previous_headings":"Drawing pedigrees","what":"Built-in pedigrees","title":"QuickPed - a free online pedigree creator","text":"left-panel QuickPed user may choose among selection standard pedigrees, including trios, full/half siblings, avuncular cousin pedigrees different kinds. Also included variety complex pedigree structures like double cousins quad half first cousins. Finally, following historic pedigrees available: Habsburg: subset infamously inbred family tree Habsburg royalties. inbreeding coefficient King Charles II Spain (1661-1700) approximately 0.25, .e., equivalent child produced full siblings. Pedigree adapted Wikipedia. See also Role Inbreeding Extinction European Royal Dynasty. Jicaque: pedigree Jicaque Indians originally studied Chapman & Jacquard (1971) subsequently used many papers relatedness pedigree coefficients. Queen Victoria (haemophilia): royal family tree descending Queen Victoria, showing X-linked inheritance haemophilia. Adapted Figure S1 Genotype Analysis Identifies Cause “Royal Disease”. Tutankhamun: family tree Egyptian pharaoh Tutankhamun, inferred genetic evidence presented Hawass et al. (2010), Ancestry Pathology King Tutankhamun’s Family.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"ped-files","dir":"Articles > Web_only","previous_headings":"","what":"Ped files","title":"QuickPed - a free online pedigree creator","text":"useful feature QuickPed produce text files describing pedigrees -called ped format. files often required software pedigree analysis. simple illustration, consider pedigree: text file describing pedigree may contain following. columns : id: Individual ID fid: Father’s ID (0 included pedigree) mid: Mother’s ID (0 included pedigree) sex: Sex (1 = male; 2 = female; 0 = unknown) aff: Affection status (1 = unaffected; 2 = affected; 0 = unknown) noted ped format completely standardised, different software may use slightly different versions. example, first column Family ID sometimes required. Also, aff column may needed non-medical applications. details may specified using QuickPed. pedigree information may shown plot, stored ped file. current version QuickPed, includes twin relationships, carrier status deceased status.","code":"id fid mid sex aff 1 0 0 1 1 2 0 0 2 1 3 1 2 2 2"},{"path":[]},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"overview","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"Overview","title":"QuickPed - a free online pedigree creator","text":"Relationships four buttons offering different analyses relationships within loaded pedigree. buttons , order: Describe relationship. Prints standardised description relationship two selected individuals. text generated verbalisr. Calculate coefficients. Prints important relatedness coefficients two selected individuals: inbreeding coefficient individual. kinship coefficient φ\\varphi. degree relationship. IBD coefficients κ=(κ0,κ1,κ2)\\kappa = (\\kappa_0, \\kappa_1, \\kappa_2), individuals non-inbred. condensed identity coefficients Δ=(Δ1,...,Δ9)\\Delta = (\\Delta_1, ..., \\Delta_9), either individual inbred. Relatedness triangle. Produces plot representing IBD coefficients κ\\kappa point relatedness triangle. Requires two noninbred individuals selected. Table coefficients. Activates popup window user can choose among variety coefficients, including detailed identity X-chromosomal coefficients, computed pair pedigree members. Generates tab-separated file download.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"coefficients-of-relatedness","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"Coefficients of relatedness","title":"QuickPed - a free online pedigree creator","text":"QuickPed calculates variety different relatedness coefficients, briefly review convenience. details recommend e.g. Thompson’s book Statistical Inference Genetic Data Pedigrees Lange’s book Mathematical Statistical Methods Genetic Analysis. given pedigree members AA BB define following: inbreeding coefficient ff individual AA kinship coefficient (see ) parents AA, 0 AA founder pedigree. kinship coefficient φ\\varphi AA BB probability random allele AA random allele BB locus, identical descent (IBD), .e., ancestral origin within pedigree. IBD coefficients κ=(κ0,κ1,κ2)\\kappa = (\\kappa_0, \\kappa_1, \\kappa_2) AA BB, probabilities sharing respectively 0, 1, 2 alleles IBD random locus. Defined noninbred individuals . condensed identity coefficients Δ=(Δ1,…,Δ9)\\Delta = (\\Delta_1, \\dots, \\Delta_9) AA BB, expected relative frequencies 9 condensed IBD states (see ) four homologue alleles autosomal locus. detailed identity coefficients δ=(δ1,…,δ15)\\delta = (\\delta_1, \\dots, \\delta_{15}) expected relative frequencies 15 detailed IBD states (see ).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"a-brief-recap-of-identity-states","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"A brief recap of identity states","title":"QuickPed - a free online pedigree creator","text":"Following Jacquard (1974) subsequent authors, 4 alleles carried individuals AA BB autosomal locus, can drawn dots square diagram: identity state pattern IBD alleles, represented line segments connecting alleles.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"detailed-states","dir":"Articles > Web_only","previous_headings":"Relatedness analysis > A brief recap of identity states","what":"Detailed states","title":"QuickPed - a free online pedigree creator","text":"total 15 possible patterns IBD 4 alleles. called detailed identity states, shown order used QuickPed.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"condensed-states","dir":"Articles > Web_only","previous_headings":"Relatedness analysis > A brief recap of identity states","what":"Condensed states","title":"QuickPed - a free online pedigree creator","text":"applications paternal/maternal origin alleles matter. 15 detailed states reduced 9, known condensed identity states:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"x-chromosomal-identity-coefficients","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"X-chromosomal identity coefficients","title":"QuickPed - a free online pedigree creator","text":"X-chromosomal identity states coefficients less studied autosomal ones, fewer conventions regarding order draw . presentation claim superiority others; main purpose act reference understanding output QuickPed. autosomal case, identity coefficients X expected proportions possible IBD states involving alleles random locus (X). challenge set states depends sex two individuals: F/F, F/M, M/F M/M (F = female M = male). Males hemizygous X, one allele locus (except -called pseudo-autosomal regions, ignore ). Hence, pairs individuals including male, total number alleles less 4. However, avoid memorise new states sex combination, may re-use autosomal pictograms invoking simple rule: Given X-chromosomal identity state, replace hemizygous allele pair autozygous alleles. rule guides following table, shows interpret condensed X-chromosomal coefficients returned QuickPed. first row, corresponding two females, identical autosomal case. similar fashion, states corresponding detailed X-chromosomal coefficients, follows: Note hemizygous males, single allele drawn right side, since maternally inherited. also noted QuickPed always outputs number coefficients (9 condensed; 15 detailed), regardless sex, NAs positions corresponding undefined states.","code":""},{"path":"https://magnusdv.github.io/pedsuite/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Magnus Dehli Vigeland. Author, maintainer. Thore Egeland. Author.","code":""},{"path":"https://magnusdv.github.io/pedsuite/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Vigeland MD (2021). Pedigree Analysis R. Academic Press. ISBN 978-0128244302.","code":"@Book{, title = {Pedigree Analysis in {R}}, author = {Magnus Dehli Vigeland}, year = {2021}, publisher = {Academic Press}, isbn = {978-0128244302}, }"},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"the-pedsuite-r-packages-for-pedigree-analysis","dir":"","previous_headings":"","what":"R packages for pedigree analysis","title":"R packages for pedigree analysis","text":"pedsuite collection R packages pedigree analysis, covering variety applications across several fields. packages designed work harmoniously together, often allowing complex tasks solved lines code.","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"core-packages","dir":"","previous_headings":"","what":"Core packages","title":"R packages for pedigree analysis","text":"centre pedsuite find package pedtools, others depend. addition, several packages contain basic features often needed many types analysis. core packages: pedtools: Creating working pedigrees marker data forrel: Forensic pedigree analysis relatedness analysis pedprobr: Marker probabilities pedigree likelihoods ribd: Computation pedigree-based relatedness coefficients verbalisr: Verbal descriptions pedigree relationships","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"specialised-packages","dir":"","previous_headings":"","what":"Specialised packages","title":"R packages for pedigree analysis","text":"following packages devoted special applications: ibdsim2: Simulation identity--descent sharing family members dvir: Disaster victim identification paramlink2: Parametric linkage analysis pedbuildr: Pedigree reconstruction pedFamilias: Import export .fam files used Familias software pedmut: Mutation models pedigree likelihood computations segregatr: Segregation analysis clinical variant interpretation","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"retired-packages","dir":"","previous_headings":"","what":"Retired packages","title":"R packages for pedigree analysis","text":"packages superseded packages longer compatible rest pedsuite. maintained legacy purposes used new projects. paramlink: package marked birth pedsuite. Originally intended parametric linkage analysis, also contained seeds current packages pedtools, pedprobr, ribd forrel. IBDsim: replaced ibdsim2. (Regrettably, name ‘IBDsim’ similar unrelated (non-R) software ‘IBDSim’ (Leblois, Estoup & Rousset).)","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"imported-packages","dir":"","previous_headings":"","what":"Imported packages","title":"R packages for pedigree analysis","text":"kinship2: Pedigree plotting pedsuite depends kinship2 (Sinnwell, Therneau & Schaid) pedigree alignment calculations.","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"shiny-apps","dir":"","previous_headings":"","what":"Shiny apps","title":"R packages for pedigree analysis","text":"Several Shiny apps based pedsuite developed. Read : QuickPed: Interactive pedigree builder relatedness analyser DIVIANA: Disaster victim identification ibdsim2-shiny: IBD distributions pedigrees KLINK: Kinship analysis linked markers LinkageLab: Playing linked markers ibdClassifier: Classifying relationships based IBD segments","code":""},{"path":"https://magnusdv.github.io/pedsuite/reference/pedsuite-package.html","id":null,"dir":"Reference","previous_headings":"","what":"pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis — pedsuite-package","title":"pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis — pedsuite-package","text":"'pedsuite' collection packages pedigree analysis, covering applications forensic genetics, medical genetics . detailed presentation 'pedsuite' given book 'Pedigree Analysis R' (Vigeland, 2021, ISBN: 9780128244302).","code":""},{"path":[]},{"path":"https://magnusdv.github.io/pedsuite/reference/pedsuite-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis — pedsuite-package","text":"Maintainer: Magnus Dehli Vigeland m.d.vigeland@medisin.uio.(ORCID) Authors: Thore Egeland thore.egeland@nmbu.(ORCID)","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-131","dir":"Changelog","previous_headings":"","what":"pedsuite 1.3.1","title":"pedsuite 1.3.1","text":"CRAN release: 2024-09-06 New package: pedFamilias Add several app homepages Minor code updates","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-120","dir":"Changelog","previous_headings":"","what":"pedsuite 1.2.0","title":"pedsuite 1.2.0","text":"CRAN release: 2023-06-26 Update Github Actions workflow Update pkgdown stuff Various minor improvements Add citation info","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-110","dir":"Changelog","previous_headings":"","what":"pedsuite 1.1.0","title":"pedsuite 1.1.0","text":"CRAN release: 2022-01-07 Include verbalisr core package Remove pedmut core package Fix CRAN note namespaces imported Minor README changes","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-104","dir":"Changelog","previous_headings":"","what":"pedsuite 1.0.4","title":"pedsuite 1.0.4","text":"CRAN release: 2021-06-21 Initial CRAN version","code":""}] +[{"path":"https://magnusdv.github.io/pedsuite/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://magnusdv.github.io/pedsuite/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://magnusdv.github.io/pedsuite/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://magnusdv.github.io/pedsuite/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started with the pedsuite","text":"following command installs latest official versions pedsuite packages: Alternatively, can install development versions GitHub: need packages, may choose install individually instead entire collection.","code":"install.packages(\"pedsuite\") # install.packages(\"devtools\") devtools::install_github(\"magnusdv/pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"a-quick-tour","dir":"Articles","previous_headings":"","what":"A quick tour","title":"Getting started with the pedsuite","text":"aim vignette illustrate possibilities pedsuite packages. noted barely scratching surface ; particular several packages even mentioned. comprehensive overview, recommend book. get started load pedsuite package, convenient shortcut loading core packages, making methods available current R session.","code":"library(pedsuite) #> Loading required package: forrel #> Loading required package: pedtools #> Loading required package: pedprobr #> Loading required package: ribd #> Loading required package: verbalisr"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"create-a-pedigree-pedtools","dir":"Articles","previous_headings":"A quick tour","what":"1. Create a pedigree (pedtools)","title":"Getting started with the pedsuite","text":"begin creating plotting pedigree child first cousins: symmetry let us change sex individual 3. also take opportunity showcase plot options (many available - see help page typing ?plotmethods):","code":"x = cousinPed(1, child = TRUE) plot(x) x = swapSex(x, ids = 3) #> Changing sex of spouses as well: 4 plot(x, hatched = 9, carrier = 7:8, fill = list(pink = 1), textAnnot = list(inside = c(\"1\" = \"?\")))"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"calculate-the-inbreeding-coefficient-ribd","dir":"Articles","previous_headings":"A quick tour","what":"2. Calculate the inbreeding coefficient (ribd)","title":"Getting started with the pedsuite","text":"inbreeding coefficient ff pedigree member defined probability autozygosity random autosomal locus. , probability two homologous alleles origin within pedigree. child first cousins one can work pen paper f=1/16f = 1/16. Alternatively, can calculate ribd function inbreeding(). output agrees f=1/16f = 1/16.","code":"inbreeding(x, ids = 9) #> [1] 0.0625"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"realised-inbreeding-ibdsim2","dir":"Articles","previous_headings":"A quick tour","what":"3. Realised inbreeding (ibdsim2)","title":"Getting started with the pedsuite","text":"particular child first cousins, actual autozygous fraction genome (except X & Y) called coefficient realised inbreeding, denoted fRf_R. may deviate substantially pedigree-based expectation f=1/16f = 1/16. can simulate distribution fRf_R ibdsim2 package. Since core package must load separately. First, use function ibdsim() simulate recombination process entire pedigree, 200 times: Now extract autozygous segments simulation. summary first 6 simulations, including number segments various length statistics: histogram realised inbreeding coefficients (given right-column ): see, distribution centres around expectation f=1/16=0.0625f = 1/16 = 0.0625 (red vertical line) substantial spread. sample standard deviation can found fr$stDev, case 0.02.","code":"library(ibdsim2) sims = ibdsim(x, N = 200, seed = 123) #> Simulation parameters: #> Simulations : 200 #> Chromosomes : 1-22 #> Genome length: 2753.93 Mb #> 2602.29 cM (male) #> 4180.42 cM (female) #> Recomb model : chi #> Target indivs: 1-9 #> Skip recomb : - #> Total time used: 1.82 secs fr = realisedInbreeding(sims, id = 9) head(fr$perSimulation) #> nSeg meanLen totLen maxLen minLen fReal #> 1 11 19.05892 209.6481 37.60149 0.8069583 0.06181840 #> 2 12 14.17339 170.0807 48.43095 1.3405519 0.05015126 #> 3 12 12.87321 154.4785 26.10949 0.1452881 0.04555068 #> 4 19 17.44059 331.3712 58.63821 1.2124618 0.09771059 #> 5 16 16.95554 271.2886 44.95560 1.0034634 0.07999419 #> 6 13 17.84055 231.9271 49.91405 0.9327245 0.06838775 hist(fr$perSimulation$fReal, xlim = c(0, 0.15), breaks = 16, xlab = \"f_R\", main = NULL) # Expected value abline(v = 1/16, col = 2)"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"marker-simulation-forrel","dir":"Articles","previous_headings":"A quick tour","what":"4. Marker simulation (forrel)","title":"Getting started with the pedsuite","text":"Note everything done far purely theoretical, markers involved. medical forensic applications usually work genetic data form marker genotypes, let us simulate dataset family. markerSim() function forrel package simulates genotypes pedigree members specific type markers. instance, produce 500 SNPs alleles B (equally frequent, default): can see genotypes first markers printing y console.","code":"y = markerSim(x, N = 500, alleles = c(\"A\", \"B\")) #> Unconditional simulation of 500 autosomal markers. #> Individuals: 1, 2, 3, 4, 5, 6, 7, 8, 9 #> Allele frequencies: #> A B #> 0.5 0.5 #> Mutation model: No #> #> Simulation finished. #> Calls to `likelihood()`: 0. #> Total time used: 0 seconds. y #> id fid mid sex <1> <2> <3> <4> <5> #> 1 * * 1 A/B B/B A/A B/B A/A #> 2 * * 2 A/B A/B A/B A/A A/B #> 3 1 2 2 A/B A/B A/B A/B A/B #> 4 * * 1 A/B A/B B/B A/B A/B #> 5 1 2 1 B/B A/B A/B A/B A/A #> 6 * * 2 A/B B/B A/A A/B A/A #> 7 4 3 1 B/B A/A B/B A/B A/B #> 8 5 6 2 A/B A/B A/B B/B A/A #> 9 7 8 1 B/B A/A B/B B/B A/A #> Only 5 (out of 500) markers are shown."},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"inference-of-pairwise-relationships-forrel","dir":"Articles","previous_headings":"A quick tour","what":"5. Inference of pairwise relationships (forrel)","title":"Getting started with the pedsuite","text":"real dataset, natural quality control step check correctness pedigree. One way use data estimate pairwise relationship, compare result pedigree. function checkPairwise() , presents result relationship triangle. plot shows pairwise estimates near expected location triangle.","code":"checkPairwise(y) #> Excluding inbred individuals: 9"},{"path":"https://magnusdv.github.io/pedsuite/articles/pedsuite.html","id":"where-to-go-from-here","dir":"Articles","previous_headings":"","what":"Where to go from here","title":"Getting started with the pedsuite","text":"enjoyed quick tour like details, check GitHub README files packages interest , instance: pedtools: Creating working pedigrees marker data forrel: Forensic pedigree analysis relatedness analysis ribd: Computation pedigree-based relatedness coefficients verbalisr: Verbal descriptions pedigree relationships ibdsim2: Simulation identity--descent sharing family members dvir: Disaster victim identification Try interactive pedigree builder QuickPed: https://magnusdv.shinyapps.io/quickped. pedtools vignette contains details pedigree objects R plot manipulate .","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"learning-outcomes","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcomes","title":"GHEP Online School 2024: Workshop 1","text":"Classical concepts methods genetic relatedness Using QuickPed apps pedigree analysis Using Familias software perform kinship testing Methods relationship inference pedigree reconstruction Practical methods disaster victim identification","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"software-preparation-r","dir":"Articles > Web_only","previous_headings":"","what":"Software preparation: R","title":"GHEP Online School 2024: Workshop 1","text":"Several exercises use R. order , please install following computer: recent version R RStudio Run following command R install pedsuite packages:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"software-preparation-familias","dir":"Articles > Web_only","previous_headings":"","what":"Software preparation: Familias","title":"GHEP Online School 2024: Workshop 1","text":"Part course based kinship testing Familias software, can installed : https://familias./download.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"GHEP Online School 2024: Workshop 1","text":"course runs Monday October 2024, 16 20 (CEST). following schedule tentative:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-7-theory-of-relatedness","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 7: Theory of relatedness","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 Introduction pedigrees, QuickPed R (MDV) 17:00–17:45 Exercises . (Solutions) 17:45–18:00 Break 18:00–19:00 Measures relatedness (MDV) 19:00–19:45 Exercises II. (Solutions) 19:45–20:00 Wrap-","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-14-kinship-testing","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 14: Kinship testing","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 Introduction forensic kinship testing (TE) 17:00–17:45 Exercises III. (Solutions) 17:45–18:00 Break 18:00–19:00 Kinship testing Familias (TE) 19:00–19:45 Exercises IV. File needed: kinship-riddle.fam. (Solutions) 19:45–20:00 Wrap-","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-21-relatedness-inference","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 21: Relatedness inference","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 Realised relatedness: siblings alike others? (MDV) 17:00–17:45 Exercises V. (Solutions) 17:45–18:00 Break 18:00–19:00 Pedigree reconstruction (MDV) 19:00–19:45 Exercises VI 19:45–20:00 Wrap-","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html","id":"oct-28-disaster-victim-identification","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Oct 28: Disaster victim identification","title":"GHEP Online School 2024: Workshop 1","text":"16:00–17:00 DNA-based disaster victim identification (TE) 17:00–17:45 Exercises VII 17:45–18:00 Break 18:00–19:00 Practical DVI Diviana (MDV) 19:00–19:45 Exercises VIII 19:45–20:00 Wrap-Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"description","dir":"Articles > Web_only","previous_headings":"","what":"Description","title":"ISFG Summer School - Virtual Edition 2021","text":"study genetic relatedness genetic information flows families, central variety research fields, including medical forensic genetics. aim course introduce elegant statistical foundations relatedness, well several forensic applications, particular focus using R calculations visualisations. lectures exercises based book Pedigree Analysis R. 30% discount available participants (buy book order attend course).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcome","title":"ISFG Summer School - Virtual Edition 2021","text":"completing course participants knowledge : Classical concepts methods statistical genetics relatedness analysis create, manipulate plot pedigrees R compute pedigree likelihoods likelihood ratios R perform kinship testing pedigree reconstruction R perform disaster victim identification R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"","what":"Prerequisites","title":"ISFG Summer School - Virtual Edition 2021","text":"Basic knowledge genetics probability. previous experience R recommended. Please make sure R (version > 4.0) installed computer. recommend running R RStudio. following R command installs pedsuite packages, used throughout course:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"ISFG Summer School - Virtual Edition 2021","text":"course runs 14 18 (CEST) day, 15 minute break middle. lectures aimed 55 minutes, allowing short interval exercises.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"day-1-july-28-wednesday","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Day 1 — July 28 (Wednesday)","title":"ISFG Summer School - Virtual Edition 2021","text":"14:00–15:00 Lecture 1. Introductions (MDV) 15:00–15:45 Exercise set 1 15:45–16:00 Break 16:00–17:00 Lecture 2. Working pedigrees R (MDV) 17:00–18:00 Exercise set 2","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"day-2-july-29-thursday","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Day 2 — July 29 (Thursday)","title":"ISFG Summer School - Virtual Edition 2021","text":"14:00–15:00 Lecture 3. Kinship testing: paternity cases complex cases (TE) 15:00–15:45 Exercise set 3 15:45–16:00 Break 16:00–17:00 Lecture 4. Relatedness coefficients (MDV) 17:00–18:00 Exercise set 4","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2021.html","id":"day-3-july-30-friday","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Day 3 — July 30 (Friday)","title":"ISFG Summer School - Virtual Edition 2021","text":"14:00–15:00 Lecture 5. Relatedness inference pedigree reconstruction (MDV) 15:00–15:45 Exercise set 5 15:45–16:00 Break 16:00–17:00 Lecture 6. Disaster victim identification forensic applications (TE) 17:00–18:00 Exercise set 6 Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"description","dir":"Articles > Web_only","previous_headings":"","what":"Description","title":"ISFG Summer School 2023","text":"study genetic relatedness flow genetic information within families, central forensic genetics. aim course introduce elegant statistical foundations relatedness, explore important forensic applications. use software R calculations visualisations, particular pedsuite packages pedigree analysis. lectures exercises based book Pedigree Analysis R (need book order attend course).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcome","title":"ISFG Summer School 2023","text":"completing course participants knowledge : Classical concepts statistical genetics relatedness analysis produce informative beautiful pedigree plots compute coefficients relatedness perform kinship testing pedigree reconstruction R perform disaster victim identification R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"","what":"Prerequisites","title":"ISFG Summer School 2023","text":"Basic knowledge genetics probability previous experience R recommended, strictly required recent version R (least 4.1) must installed computer recommend running R RStudio following R command installs pedsuite packages, used throughout course:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"ISFG Summer School 2023","text":"course runs 18 22 (CEST) day, 15 minute break middle. following schedule tentative:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"aug-30-wednesday-pedigree-analysis-basic","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Aug 30 (Wednesday) – Pedigree analysis: Basic","title":"ISFG Summer School 2023","text":"18:00–19:00 Pedigrees measures relatedness (MDV) 19:00–19:15 Crash course R (MDV) 19:15–20:00 Exercises 20:00–20:15 Break 20:15–21:00 Kinship testing (TE) 21:00–21:45 Exercises II 21:45–22:00 Summary discussion","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2023.html","id":"aug-31-thursday-pedigree-analysis-advanced","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Aug 31 (Thursday) – Pedigree analysis: Advanced","title":"ISFG Summer School 2023","text":"18:00–19:00 Relatedness inference pedigree reconstruction (MDV) 19:00–19:45 Exercises III 19:45–20:00 Break 20:00–21:00 Disaster victim identification (TE) 21:00–21:45 Exercises IV 21:45–22:00 Summary discussion Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"kinship-statistics-and-pedigree-analysis","dir":"Articles > Web_only","previous_headings":"","what":"Kinship Statistics and Pedigree Analysis","title":"ISFG Congress 2024 Workshop","text":"Date: Tuesday, 10th September, 2024 : San Francisco Hotel Monumento, Santiago de Compostela, Spain Teachers: Magnus Dehli Vigeland Thore Egeland ISFG 2024 workshops: https://isfg2024.com/pre-congress-workshops/","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"description","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Description","title":"ISFG Congress 2024 Workshop","text":"study pedigrees genetic relatedness central forensic genetics. aim course introduce elegant statistical foundations relatedness, well several forensic applications. certain parts use R calculations visualisations. basic session focus pedigree coefficients likelihood ratios kinship analysis. addition, demonstrate QuickPed, online tool creating pedigrees computing relatedness: https://magnusdv.shinyapps.io/quickped advanced part explore recently developed methods implementations Disaster Victim Identification (DVI) pedigree reconstruction. course material based book Pedigree Analysis R (Vigeland ’21) selected papers. session alternate lectures hands-exercises. Solutions exercises provided discussed end session. Attendance ‘Basic session’ required ‘Advanced session’ participants familiar R.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Learning outcome","title":"ISFG Congress 2024 Workshop","text":"completing course participants knowledge : Classical concepts statistical genetics relatedness analysis produce informative beautiful pedigree plots compute coefficients relatedness perform kinship testing pedigree reconstruction R perform disaster victim identification R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Prerequisites","title":"ISFG Congress 2024 Workshop","text":"Basic knowledge genetics probability participants must bring laptop administrative rights recent version R (least 4.1) must installed computer previous experience R recommended, strictly required strongly recommend running R RStudio","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis","what":"Schedule","title":"ISFG Congress 2024 Workshop","text":"workshop run full-day course Tuesday 10th, 9 18:30 (CEST). following schedule tentative:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"morning-session-pedigree-analysis-basic","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis > Schedule","what":"Morning session – Pedigree analysis: Basic","title":"ISFG Congress 2024 Workshop","text":"09:00–10:00 Pedigrees measures relatedness (MDV) 10:00–11:00 Exercises 11:00–11:15 Break 11:15–12:00 Kinship testing (TE) 12:00–12:45 Exercises II 12:45–13:00 Summary discussion Lunch break 13:00 - 14:30","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html","id":"afternoon-session-pedigree-analysis-advanced","dir":"Articles > Web_only","previous_headings":"Kinship Statistics and Pedigree Analysis > Schedule","what":"Afternoon session – Pedigree analysis: Advanced","title":"ISFG Congress 2024 Workshop","text":"14:30–15:30 Relatedness inference pedigree reconstruction (MDV) 15:30–16:15 Exercises III 16:15–16:30 Break 16:30–17:30 Disaster victim identification (TE) 17:30–18:15 Exercises IV 18:15–18:30 Summary discussion Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"summary","dir":"Articles > Web_only","previous_headings":"","what":"Summary","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"Title: Statistical methods relatedness pedigree analysis Dates: 13–17 June 2022 Teachers: Magnus Dehli Vigeland Thore Egeland : Room 2203a (“Helix”), Kristine Bonnevies hus, University Oslo Address: Blindernveien 31, entrance Moltke Moes vei. Credits: 4 ECTS Exam: Home project (passed/passed)","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"description","dir":"Articles > Web_only","previous_headings":"","what":"Description","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"course introduces statistical methods used relatedness pedigree analysis, applications forensic genetics, medical genetics pedigree reconstruction. study genetic relatedness genetic information flows families, central variety important research fields, including medical genetics, forensics animal breeding. aim course introduce students elegant concepts results forming theoretical foundation genetic relatedness, present detail several modern applications. exercises use R pedsuite packages pedigree analysis visualisation. Much course material based book Pedigree Analysis R may interest participants (required attend course).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"","what":"Learning outcome","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"completing course participants knowledge : Classical concepts methods statistical genetics relatedness analysis Important applications pedigree analysis, including forensic kinship analysis, medical segregation analysis pedigree reconstruction work pedigrees R","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"","what":"Prerequisites","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"Basic knowledge genetics probability. previous experience R recommended, strictly required. Please make sure R (version > 4.1) installed computer. strongly recommend running R RStudio. following R command installs pedsuite packages, used throughout course:","code":"install.packages(\"pedsuite\")"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"","what":"Schedule","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"course runs 9 16.30 (CEST) day. tentative schedule given . Minor changes may occur.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"monday-june-13","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Monday, June 13","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Introduction : Pedigrees, genetics probabilities (MDV) 11–12 Exercises 12–13 Lunch 13–15 Introduction II: R pedsuite (MDV) 15–16:30 Exercises II","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"tuesday-june-14","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Tuesday, June 14","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Relatedness : IBD coefficients relatedness (MDV) 11–12 Exercises III 12–13 Lunch 13–15 Relatedness II: Realised relatedness (MDV) 15–16:30 Exercises IV","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"wednesday-june-15","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Wednesday, June 15","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Forensic applications (TE) 11–12 Exercises V 12–13 Lunch 13–15 Inference relatedness pedigree reconstruction (MDV) 15–16:30 Exercises VI","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"thursday-june-16","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Thursday, June 16","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Forensic applications II (TE) 11–12 Exercises VII 12–13 Lunch 13–15 Linkage segregation analysis medical genetics (MDV) 15–16:30 Exercises VIII","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-norbis2022.html","id":"friday-june-17","dir":"Articles > Web_only","previous_headings":"Schedule","what":"Friday, June 17","title":"Statistical methods in relatedness and pedigree analysis - 2022","text":"09–11 Genealogical triangulation (TE/MDV) 11–12 Exercises 12–13 Lunch 13–16:30 Case study wrap (MDV) Comments questions may sent magnusdv medisin uio .","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"workshop-genetic-relatedness","dir":"Articles > Web_only","previous_headings":"","what":"Workshop: Genetic relatedness","title":"Young Investigator Day 2024","text":"Date: Monday 14th October, 2024 : Cancer Registry Norway Teacher: Magnus Dehli Vigeland Part NOFE conference (Norwegian Epidemiological Association)","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"description","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Description","title":"Young Investigator Day 2024","text":"study pedigrees genetic relatedness central many fields, including medical genetics, forensics epidemiology. aim course introduce elegant statistical foundations relatedness, well relevant software tools. workshop alternate lectures hands-exercises. exercises use R, others use QuickPed, free online tool creating analysing pedigrees: https://magnusdv.shinyapps.io/quickped course material based book Pedigree Analysis R (Vigeland ’21), may point reference participants want delve deeper subject.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"learning-outcome","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Learning outcome","title":"Young Investigator Day 2024","text":"completing course participants knowledge : Classical concepts statistical genetics relatedness analysis produce informative beautiful pedigree plots compute coefficients relatedness siblings related others","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"prerequisites","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Prerequisites","title":"Young Investigator Day 2024","text":"Basic knowledge genetics probability participants must bring laptop recent version R installed (least 4.3.0) strongly recommend running R RStudio","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html","id":"schedule","dir":"Articles > Web_only","previous_headings":"Workshop: Genetic relatedness","what":"Schedule","title":"Young Investigator Day 2024","text":"workshop run half-day course, 12 16, following (tentative) schedule: 12:00–13:00 Introduction pedigrees relationships 13:00–13:45 Exercises . (Solutions) 13:45–14:00 Break 14:00–15:00 Measures relatedness 15:00–15:45 Exercises II. (Solutions) 15:45–16:00 Summary discussion Comments questions may sent magnusdv gmail dot com.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"upcoming-events","dir":"Articles > Web_only","previous_headings":"","what":"Upcoming events","title":"Talks and courses based on the pedsuite","text":"Oct 7,14,21 28, 2024. Kinship pedigree analysis: Methods applications. Four-part lecture series, part ISFG-GHEP Online School 2024. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage.","code":""},{"path":[]},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section","dir":"Articles > Web_only","previous_headings":"Past events","what":"2024","title":"Talks and courses based on the pedsuite","text":"Oct 15. DIVIANA: free, user-friendly app complex DVI cases. Research seminar RMF, Storo, Oslo. Speaker: Magnus D. Vigeland. Oct 14. Genetic Relatedness. Half-day workshop Young Investigator Day NOFE Conference. Lecturer: Magnus D. Vigeland. Course homepage. Oct 10. DIVIANA: free, user-friendly app complex DVI cases. Invited online talk 2nd Intl Symposium DNA Supported Missing Persons Disaster Victim Identification, Tbilisi, Georgia. Speaker: Magnus D. Vigeland. Slides (extended version ISFG talk). Sept 24. Advanced Theoretical Challenges: Kinship. Presentation solutions results theoretical proficiency test prepared ISFG-GHEP 2024. Exercises. Presentation. Sept 11. DIVIANA: free, user-friendly app complex DVI cases. Oral presentation ISFG Congress 2024, Santiago de Compostela. Speaker: Magnus D. Vigeland. Slides. Sept 10. Kinship statistics pedigree analysis. Pre-congress workshop, ISFG Congress 2024, Santiago de Compostela. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-1","dir":"Articles > Web_only","previous_headings":"Past events","what":"2023","title":"Talks and courses based on the pedsuite","text":"Aug 30-31. Pedigree Analysis. ISFG Summer School 2023. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-2","dir":"Articles > Web_only","previous_headings":"Past events","what":"2022","title":"Talks and courses based on the pedsuite","text":"June 13-17. Statistical methods relatedness pedigree analysis. NORBIS 1-week intensive course, Oslo, Norway. Teachers: Magnus D. Vigeland Thore Egeland. Course homepage. Lecture: Pedigrees relatedness analysis R Lecture: Introduction pedsuite Exercises 1: Pedigree analysis R Exercises 2: Forensic case studies","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-3","dir":"Articles > Web_only","previous_headings":"Past events","what":"2021","title":"Talks and courses based on the pedsuite","text":"Lecture 1: enough data? Lecture 2: exhumed? Jul 28-30. Pedigree Analysis R. ISFG Summer School - Virtual Edition 2021. Teachers: Thore Egeland Magnus D. Vigeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-4","dir":"Articles > Web_only","previous_headings":"Past events","what":"2020","title":"Talks and courses based on the pedsuite","text":"Jan 06-10. Statistical methods relatedness pedigree analysis. NORBIS 1-week intensive course, Oslo, Norway. Teachers: Thore Egeland Magnus D. Vigeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-5","dir":"Articles > Web_only","previous_headings":"Past events","what":"2018","title":"Talks and courses based on the pedsuite","text":"Jan 08-12. Statistical methods relatedness pedigree analysis. NORBIS 1-week intensive course, Oslo, Norway. Teachers: Thore Egeland Magnus D. Vigeland. Details program.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/courses.html","id":"section-6","dir":"Articles > Web_only","previous_headings":"Past events","what":"2016","title":"Talks and courses based on the pedsuite","text":"Nov 16-19. Statistical methods genetics using R. 4-day intensive course, Rio de Janeiro, Brazil. Teachers: Thore Egeland Magnus D. Vigeland. Course homepage.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/diviana.html","id":"what-is-diviana","dir":"Articles > Web_only","previous_headings":"","what":"What is DIVIANA?","title":"DIVIANA","text":"DIVIANA user-friendly app disaster victim identification (DVI).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/ibdClassifier.html","id":"what-is-ibdclassifier","dir":"Articles > Web_only","previous_headings":"","what":"What is ibdClassifier?","title":"ibdClassifier","text":"ibdClassifier tool predicting pairwise relationship based set IBD segments. implements Bayes classifier using number segments lengths.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/ibdClassifier.html","id":"note-still-under-development","dir":"Articles > Web_only","previous_headings":"What is ibdClassifier?","what":"Note: Still under development","title":"ibdClassifier","text":"ibdClassifier experimental app currently development. yet ready used critical real-world applications.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/ibdsim2shiny.html","id":"what-is-ibdsim2-shiny","dir":"Articles > Web_only","previous_headings":"","what":"What is ibdsim2-shiny?","title":"ibdsim2-shiny","text":"online tool visualising comparing distributions IBD-sharing pedigree members.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/klink.html","id":"what-is-klink","dir":"Articles > Web_only","previous_headings":"","what":"What is KLINK?","title":"KLINK - kinship with linked markers","text":"KLINK user-friendly app extending Familias software kinship calculations forensic genetics. Unlike Familias, KLINK allows pairs linked markers, often seen modern marker kits. KLINK substantial overlap Familias companion FamLink, offers several unique features: platform independent (Windows) visualisations pedigrees marker maps ready--use output reports Excel format noted KLINK currently handles pairs linked markers. general linkage, e.g. dense SNPs, recommend FamLink.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/klink.html","id":"running-klink","dir":"Articles > Web_only","previous_headings":"","what":"Running KLINK","title":"KLINK - kinship with linked markers","text":"KLINK available online app R package. latter important sensitive data want run everything locally. set , simply install CRAN can open KLINK command","code":"install.packages(\"KLINK\") KLINK::launchApp()"},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/linkagelab.html","id":"what-is-linkagelab","dir":"Articles > Web_only","previous_headings":"","what":"What is LinkageLab?","title":"LinkageLab - playing with linked markers","text":"LinkageLab pedagogical tool understanding marker linkage affects likelihood ratios (LRs) kinship testing.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"book","dir":"Articles > Web_only","previous_headings":"","what":"Book","title":"Publications featuring the pedsuite","text":"book Pedigree Analysis R (Academic Press, 2021) based pedsuite contains detailed explanations examples use different packages.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"papers","dir":"Articles > Web_only","previous_headings":"","what":"Papers","title":"Publications featuring the pedsuite","text":"following list publications featuring pedsuite packages. know others, please let know!","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedsuite-multiple-packages","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedsuite (multiple packages)","title":"Publications featuring the pedsuite","text":"MD Vigeland. QuickPed: online tool drawing pedigrees analysing relatedness. BMC Bioinf, 2022. M Kruijver, J-Bright. tool simulating single source mixed DNA profiles. Forensic Sci Int: Genetics, 2022. NE Altınışık, DD Kazancı, et al. genomic snapshot demographic cultural dynamism Upper Mesopotamia Neolithic Transition. Science Advances, 2022.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"dvir","dir":"Articles > Web_only","previous_headings":"Papers","what":"dvir","title":"Publications featuring the pedsuite","text":"MD Vigeland, T Egeland. Joint DNA-based disaster victim identification. Sci Rep, 2021.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"forrel","dir":"Articles > Web_only","previous_headings":"Papers","what":"forrel","title":"Publications featuring the pedsuite","text":"FL Marsico, Caridi. Incorporating non-genetic evidence large scale missing person searches: general approach beyond filtering. Forensic Sci Int: Genetics, 2023. M Iungman, S Biagini, M Canteros et al. Empirical validation family-member prioritization approach maximize statistical power missing person cases. Forensic Sci Int: Genetics Suppl Series, 2022. Chernomoretz, F Marsico, et al. Bayesian networks DNA-based kinship analysis: Functionality validation GENis missing person identification module. Forensic Sci Int: Genetics Suppl Series, 2022. HK Brustad, M Colucci, MA Jobling NA Sheehand, T Egeland. Strategies pairwise searches forensic kinship analysis. Forensic Sci Int: Genetics, 2021. FL Marsico, MD Vigeland, T Egeland, M Herrera Piñero. Making decisions missing person identification cases low statistical power. Forensic Sci Int: Genetics, 2021. HK Brustad, MD Vigeland, T Egeland. Pairwise relatedness testing context inbreeding: expectation variance likelihood ratio. Int J Legal Med, 2020. MD Vigeland, FL Marsico, M Herrera Piñero, T Egeland. Prioritising family members genotyping missing person cases: general approach combining statistical power exclusion inclusion. Forensic Sci Int: Genetics, 2020. HK Brustad, T Egeland. impact ignoring inbreeding pairwise kinship evaluations. Forensic Sci Int: Genetics Suppl Series, 2019. MD Vigeland, T Egeland. Handling founder inbreeding forensic kinship analysis. Forensic Sci Int: Genetics Suppl Series, 2019.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"ibdsim-ibdsim2","dir":"Articles > Web_only","previous_headings":"Papers","what":"IBDsim / ibdsim2","title":"Publications featuring the pedsuite","text":"C Cavagnino, G Runfeldt, et al. Unearthing Y Harewood Cemetery inference George Washington’s Y-chromosomal haplotype. iScience, 2024. H Vinje, HK Brustad, et al. Classification breed combinations slaughter pigs based genotypes—modeling DNA samples crossbreeds fuzzy sets purebred founders. Front Genet, 2023. VM Narasimhan, R Rahbari, Scally, et al. Estimating human mutation rate autozygous segments reveals population differences human mutational processes. Nat Commun, 2017. S Steinberg, S Gudmundsdottir, G Sveinbjornsson, et al. Truncating mutations RBM12 associated psychosis. Nat Genet, 2017.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"paramlink-paramlink2","dir":"Articles > Web_only","previous_headings":"Papers","what":"paramlink / paramlink2","title":"Publications featuring the pedsuite","text":"Ø Bleka, L Prieto, P Gill. EFMrep: extension EuroForMix improved combination STR DNA mixture profiles. Forensic Sci Int: Genetics, 2022. Z Bai, N Zhang, JLiu, et al. Identification missing persons kinship analysis microhaplotype sequencing single-source DNA two-person DNA mixtures. Forensic Sci Int: Genetics, 2022. F Hendrickx, Z De Corte, G Sonet, et al. masculinizing supergene underlies exaggerated male reproductive morph spider. Nature Ecology & Evolution, 2022. W Li, X Gu, C Liu, et al. synergetic effect BARD1 mutations tumorigenesis. Nat Commun, 2021. LR Lopes, S Garcia-Hernández, M Lorenzini, et al. Alpha-protein kinase 3 (ALPK3) truncating variants cause autosomal dominant hypertrophic cardiomyopathy. Eur Heart J, 2021. AL Junior, AG González, AR Vilela, et al. Genotype-phenotype correlations hypertrophic cardiomyopathy: multicenter study Portugal Spain TPM1 p.Arg21Leu variant. Rev Esp Cardiol (English Ed), 2021. G Wu, J Ruan, J Liu, et al. Variant spectrum Formin Homology 2 Domain‐Containing 3 gene Chinese patients hypertrophic cardiomyopathy. Journal American Heart Association, 2021. SL Rydning, Dudesek, F Rimmele, et al. novel heterozygous variant ERLIN2 causes autosomal dominant pure hereditary spastic paraplegia. European journal neurology, 2018. P May, S Pichler, D Hartl, et al. Rare ABCA7 variants 2 German families Alzheimer disease. Neurology Genetics, 2018. JP Ochoa, M Sabater-Molina, JM García-Pinilla, et al. Formin homology 2 domain containing 3 (FHOD3) genetic basis hypertrophic cardiomyopathy. Journal American College Cardiology, 2018. AO Tillmar, D Kling, JM Butler, et al. DNA Commission International Society Forensic Genetics (ISFG): Guidelines use X-STRs kinship analysis. Forensic Sci Int: Genetics, 2017. IL Mero, HH Mørk, Y Sheng, et al. Homozygous KIDINS220 loss--function variants fetuses cerebral ventriculomegaly limb contractures. Human Molecular Genetics, 2017. D Kling, T Egeland, M Herrera Piñero, MD Vigeland. Evaluating statistical power DNA-based identification, exemplified ‘missing grandchildren Argentina’. Forensic Sci Int: Genetics, 2017. G Dørum, D Kling, Tillmar, MD Vigeland. Mixtures relatives linked markers. Int J Legal Med, 2016. M Szopa, AH Ludwig-Galezowska, et al. family Arg103Pro mutation NEUROD1 gene detected next-generation sequencing–clinical characteristics mutation carriers. Eur J Med Gen, 2016. T Egeland, N Pinto, MD Vigeland. general approach power calculation relationship testing. Forensic Sci Int: Genetics, 2014. T Egeland, G Dørum, MD Vigeland, NA Sheehan. Mixtures relatives: pedigree perspective. Forensic Sci Int: Genetics, 2014. G Park, J Gim, AR Kim, et al. Multiphasic analysis whole exome sequencing data identifies novel mutation ACTG1 nonsyndromic hearing loss family. BMC Genomics, 2013.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedbuildr","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedbuildr","title":"Publications featuring the pedsuite","text":"Y Wei, Q Zhu, H Wang, et al. Pairwise kinship inference pedigree reconstruction using 91 microhaplotypes. Forensic Sci Int: Genetics, 2022.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedprobr","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedprobr","title":"Publications featuring the pedsuite","text":"S Bae, S Won, H Kim. Selection evaluation bi-allelic autosomal SNP markers paternity testing Koreans. Int J Legal Med, 2021.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"pedtools","dir":"Articles > Web_only","previous_headings":"Papers","what":"pedtools","title":"Publications featuring the pedsuite","text":"V Papin, G Gorjanc. Unlocking genome-based prediction selection conifers: key role within-family prediction accuracy. Preprint, 2024.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"quickped","dir":"Articles > Web_only","previous_headings":"Papers","what":"QuickPed","title":"Publications featuring the pedsuite","text":"Koch, M Slovik, et al. USP27X variants underlying X-linked intellectual disability disrupt protein function via distinct mechanisms. Life Science Alliance, 2024. R Simon, K Elísabetardóttir, G Lühke. Analysis genetic variants different horn phenotypes inheritance Icelandic sheep. Arch Anim Breed, 2024. Z Kolkova, P Durdik, et al. Identification novel RPGR mutation associated retinitis pigmentosa primary ciliary dyskinesia Slovak family: case report. Front Pediatr, 2024. TA Vaz, RM Hassunuma, et al. QUICKPED: Um breve guia de como criar rapidamente um heredograma utilizando um recurso didático -line gratuito. Rev. Multi. Educação e Meio Amb, 2024.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"ribd","dir":"Articles > Web_only","previous_headings":"Papers","what":"ribd","title":"Publications featuring the pedsuite","text":"T Nomura. Ballou’s Ancestral Inbreeding Coefficient: Formulation New Estimate Higher Reliability. Animals, 2024. MD Vigeland. Two-locus identity coefficients pedigrees. G3 Genes|Genomes|Genetics, 2023. M Kruijver, JM Curran. number alleles DNA mixtures related contributors. Forensic Sci Int: Genetics, 2022. Sharma, S Szymczak, M Rühlemann, et al. Linkage analysis identifies novel genetic modifiers microbiome traits families inflammatory bowel disease. Gut Microbes, 2022. PJ Green, J Montera. Inference complex relationships using peak height data DNA mixtures. J R Stat Soc Ser C Appl Stat, 2021. MD Vigeland. Relatedness coefficients pedigrees inbred founders. Journal Mathematical Biology, 2020.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/publications.html","id":"segregatr","dir":"Articles > Web_only","previous_headings":"Papers","what":"segregatr","title":"Publications featuring the pedsuite","text":"H-K Liu, H-L Hao, et al. Cysteinyl-tRNA Synthetase Mutation Causes Novel Autosomal-Dominant Inheritance Parkinsonism/Spinocerebellar-Ataxia Complex. Neurosci Bull, 2024. SA Schubert, D Ruano, et al. Germline variant affecting p53β isoforms predisposes familial cancer. Nat Commun, 2024. C Carrizosa, DE Undlien, MD Vigeland. shinyseg: web application flexible cosegregation sensitivity analysis. Bioinformatics, 2024. Ratajska, MD Vigeland, et al. use segregation analysis interpretation sequence variants SMAD3: case report. Molec. Genetics & Genomic Med, 2023. PM Bjørnstad, R Aaløkken, et al. 39 kb structural variant causing Lynch Syndrome detected optical genome mapping nanopore sequencing. Eur J Med Gen, 2023.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"what-is-quickped","dir":"Articles > Web_only","previous_headings":"","what":"What is QuickPed?","title":"QuickPed - a free online pedigree creator","text":"QuickPed interactive web application drawing analysing pedigrees. created pedigree may saved image text file ped format (see ). may also obtain various information pedigree, including relatedness coefficients verbal descriptions relationships. QuickPed powered pedsuite uses kinship2 alignment calculations. web app built Shiny.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"drawing-pedigrees","dir":"Articles > Web_only","previous_headings":"","what":"Drawing pedigrees","title":"QuickPed - a free online pedigree creator","text":"Creating pedigrees QuickPed intuitive: Select suitable start pedigree modify needed. may also load existing ped file (see ). Modifications done clicking one several individuals applying appropriate buttons, instance add children, siblings parents. time may change attributes like sex, affection status, twin status ID labels.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"tips-and-tricks","dir":"Articles > Web_only","previous_headings":"Drawing pedigrees","what":"Tips and tricks","title":"QuickPed - a free online pedigree creator","text":"Selecting individuals. Select/deselect pedigree members clicking . Selected individuals shown red colour. Time-saving tip: deselect everyone, click hand pointer red strikethrough. Adding parents. select single founder click “Add Parents,” new parents created individual. version 4.1.1, can also assign existing members parents. First, select child, intended parent(s) — order selection matters! Finally, click “Add Parents.” Removing individuals. removing pedigree members must decide whether want remove downwards upwards. example, pedigree , want end trio 1-2-3, select 4 /5 delete downwards ↓. Conversely, want trio 3-4-5, select 1 /2, click ↑. Note: cases, leftover founder-spouses automatically removed. Automatic labelling. Automatic labelling pedigree members available two different formats. button marked 1,2,.. applies numeric labels individuals, order appearance pedigree plot. Alternatively, -1, -2,.. button numbers members generation-wise, using Roman numerals indicate generation number. Line breaks labels. default, pedigree labels folded automatically width approximately 12 characters. insert hard line breaks, use double space. instance, want “King Lear” appear two lines, modify label “King␣␣Lear”, .e., two spaces words. Text annotation. Double clicking pedigree member opens popup window, text may added around inside symbol individual. Plot settings. pedigree gets large, increase plot region using control panel far right. may also adjust margins, size pedigree symbols text labels. R code. “R code” button, located right side QuickPed, opens text window containing R code reproduces current pedigree plot. saving .R file, simply copy-pasting code R, can explore plot options (see ?pedtools::plot.ped lots examples!) use pedigree starting point analysis pedsuite.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"built-in-pedigrees","dir":"Articles > Web_only","previous_headings":"Drawing pedigrees","what":"Built-in pedigrees","title":"QuickPed - a free online pedigree creator","text":"left-panel QuickPed user may choose among selection standard pedigrees, including trios, full/half siblings, avuncular cousin pedigrees different kinds. Also included variety complex pedigree structures like double cousins quad half first cousins. Finally, following historic pedigrees available: Habsburg: subset infamously inbred family tree Habsburg royalties. inbreeding coefficient King Charles II Spain (1661-1700) approximately 0.25, .e., equivalent child produced full siblings. Pedigree adapted Wikipedia. See also Role Inbreeding Extinction European Royal Dynasty. Jicaque: pedigree Jicaque Indians originally studied Chapman & Jacquard (1971) subsequently used many papers relatedness pedigree coefficients. Queen Victoria (haemophilia): royal family tree descending Queen Victoria, showing X-linked inheritance haemophilia. Adapted Figure S1 Genotype Analysis Identifies Cause “Royal Disease”. Tutankhamun: family tree Egyptian pharaoh Tutankhamun, inferred genetic evidence presented Hawass et al. (2010), Ancestry Pathology King Tutankhamun’s Family.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"ped-files","dir":"Articles > Web_only","previous_headings":"","what":"Ped files","title":"QuickPed - a free online pedigree creator","text":"useful feature QuickPed produce text files describing pedigrees -called ped format. files often required software pedigree analysis. simple illustration, consider pedigree: text file describing pedigree may contain following. columns : id: Individual ID fid: Father’s ID (0 included pedigree) mid: Mother’s ID (0 included pedigree) sex: Sex (1 = male; 2 = female; 0 = unknown) aff: Affection status (1 = unaffected; 2 = affected; 0 = unknown) noted ped format completely standardised, different software may use slightly different versions. example, first column Family ID sometimes required. Also, aff column may needed non-medical applications. details may specified using QuickPed. pedigree information may shown plot, stored ped file. current version QuickPed, includes twin relationships, carrier status deceased status.","code":"id fid mid sex aff 1 0 0 1 1 2 0 0 2 1 3 1 2 2 2"},{"path":[]},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"overview","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"Overview","title":"QuickPed - a free online pedigree creator","text":"Relationships four buttons offering different analyses relationships within loaded pedigree. buttons , order: Describe relationship. Prints standardised description relationship two selected individuals. text generated verbalisr. Calculate coefficients. Prints important relatedness coefficients two selected individuals: inbreeding coefficient individual. kinship coefficient φ\\varphi. degree relationship. IBD coefficients κ=(κ0,κ1,κ2)\\kappa = (\\kappa_0, \\kappa_1, \\kappa_2), individuals non-inbred. condensed identity coefficients Δ=(Δ1,...,Δ9)\\Delta = (\\Delta_1, ..., \\Delta_9), either individual inbred. Relatedness triangle. Produces plot representing IBD coefficients κ\\kappa point relatedness triangle. Requires two noninbred individuals selected. Table coefficients. Activates popup window user can choose among variety coefficients, including detailed identity X-chromosomal coefficients, computed pair pedigree members. Generates tab-separated file download.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"coefficients-of-relatedness","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"Coefficients of relatedness","title":"QuickPed - a free online pedigree creator","text":"QuickPed calculates variety different relatedness coefficients, briefly review convenience. details recommend e.g. Thompson’s book Statistical Inference Genetic Data Pedigrees Lange’s book Mathematical Statistical Methods Genetic Analysis. given pedigree members AA BB define following: inbreeding coefficient ff individual AA kinship coefficient (see ) parents AA, 0 AA founder pedigree. kinship coefficient φ\\varphi AA BB probability random allele AA random allele BB locus, identical descent (IBD), .e., ancestral origin within pedigree. IBD coefficients κ=(κ0,κ1,κ2)\\kappa = (\\kappa_0, \\kappa_1, \\kappa_2) AA BB, probabilities sharing respectively 0, 1, 2 alleles IBD random locus. Defined noninbred individuals . condensed identity coefficients Δ=(Δ1,…,Δ9)\\Delta = (\\Delta_1, \\dots, \\Delta_9) AA BB, expected relative frequencies 9 condensed IBD states (see ) four homologue alleles autosomal locus. detailed identity coefficients δ=(δ1,…,δ15)\\delta = (\\delta_1, \\dots, \\delta_{15}) expected relative frequencies 15 detailed IBD states (see ).","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"a-brief-recap-of-identity-states","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"A brief recap of identity states","title":"QuickPed - a free online pedigree creator","text":"Following Jacquard (1974) subsequent authors, 4 alleles carried individuals AA BB autosomal locus, can drawn dots square diagram: identity state pattern IBD alleles, represented line segments connecting alleles.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"detailed-states","dir":"Articles > Web_only","previous_headings":"Relatedness analysis > A brief recap of identity states","what":"Detailed states","title":"QuickPed - a free online pedigree creator","text":"total 15 possible patterns IBD 4 alleles. called detailed identity states, shown order used QuickPed.","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"condensed-states","dir":"Articles > Web_only","previous_headings":"Relatedness analysis > A brief recap of identity states","what":"Condensed states","title":"QuickPed - a free online pedigree creator","text":"applications paternal/maternal origin alleles matter. 15 detailed states reduced 9, known condensed identity states:","code":""},{"path":"https://magnusdv.github.io/pedsuite/articles/web_only/quickped.html","id":"x-chromosomal-identity-coefficients","dir":"Articles > Web_only","previous_headings":"Relatedness analysis","what":"X-chromosomal identity coefficients","title":"QuickPed - a free online pedigree creator","text":"X-chromosomal identity states coefficients less studied autosomal ones, fewer conventions regarding order draw . presentation claim superiority others; main purpose act reference understanding output QuickPed. autosomal case, identity coefficients X expected proportions possible IBD states involving alleles random locus (X). challenge set states depends sex two individuals: F/F, F/M, M/F M/M (F = female M = male). Males hemizygous X, one allele locus (except -called pseudo-autosomal regions, ignore ). Hence, pairs individuals including male, total number alleles less 4. However, avoid memorise new states sex combination, may re-use autosomal pictograms invoking simple rule: Given X-chromosomal identity state, replace hemizygous allele pair autozygous alleles. rule guides following table, shows interpret condensed X-chromosomal coefficients returned QuickPed. first row, corresponding two females, identical autosomal case. similar fashion, states corresponding detailed X-chromosomal coefficients, follows: Note hemizygous males, single allele drawn right side, since maternally inherited. also noted QuickPed always outputs number coefficients (9 condensed; 15 detailed), regardless sex, NAs positions corresponding undefined states.","code":""},{"path":"https://magnusdv.github.io/pedsuite/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Magnus Dehli Vigeland. Author, maintainer. Thore Egeland. Author.","code":""},{"path":"https://magnusdv.github.io/pedsuite/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Vigeland MD (2021). Pedigree Analysis R. Academic Press. ISBN 978-0128244302.","code":"@Book{, title = {Pedigree Analysis in {R}}, author = {Magnus Dehli Vigeland}, year = {2021}, publisher = {Academic Press}, isbn = {978-0128244302}, }"},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"the-pedsuite-r-packages-for-pedigree-analysis","dir":"","previous_headings":"","what":"R packages for pedigree analysis","title":"R packages for pedigree analysis","text":"pedsuite collection R packages pedigree analysis, covering variety applications across several fields. packages designed work harmoniously together, often allowing complex tasks solved lines code.","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"core-packages","dir":"","previous_headings":"","what":"Core packages","title":"R packages for pedigree analysis","text":"centre pedsuite find package pedtools, others depend. addition, several packages contain basic features often needed many types analysis. core packages: pedtools: Creating working pedigrees marker data forrel: Forensic pedigree analysis relatedness analysis pedprobr: Marker probabilities pedigree likelihoods ribd: Computation pedigree-based relatedness coefficients verbalisr: Verbal descriptions pedigree relationships","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"specialised-packages","dir":"","previous_headings":"","what":"Specialised packages","title":"R packages for pedigree analysis","text":"following packages devoted special applications: ibdsim2: Simulation identity--descent sharing family members dvir: Disaster victim identification paramlink2: Parametric linkage analysis pedbuildr: Pedigree reconstruction pedFamilias: Import export .fam files used Familias software pedmut: Mutation models pedigree likelihood computations segregatr: Segregation analysis clinical variant interpretation","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"retired-packages","dir":"","previous_headings":"","what":"Retired packages","title":"R packages for pedigree analysis","text":"packages superseded packages longer compatible rest pedsuite. maintained legacy purposes used new projects. paramlink: package marked birth pedsuite. Originally intended parametric linkage analysis, also contained seeds current packages pedtools, pedprobr, ribd forrel. IBDsim: replaced ibdsim2. (Regrettably, name ‘IBDsim’ similar unrelated (non-R) software ‘IBDSim’ (Leblois, Estoup & Rousset).)","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"imported-packages","dir":"","previous_headings":"","what":"Imported packages","title":"R packages for pedigree analysis","text":"kinship2: Pedigree plotting pedsuite depends kinship2 (Sinnwell, Therneau & Schaid) pedigree alignment calculations.","code":""},{"path":"https://magnusdv.github.io/pedsuite/index.html","id":"shiny-apps","dir":"","previous_headings":"","what":"Shiny apps","title":"R packages for pedigree analysis","text":"Several Shiny apps based pedsuite developed. Read : QuickPed: Interactive pedigree builder relatedness analyser DIVIANA: Disaster victim identification ibdsim2-shiny: IBD distributions pedigrees KLINK: Kinship analysis linked markers LinkageLab: Playing linked markers ibdClassifier: Classifying relationships based IBD segments","code":""},{"path":"https://magnusdv.github.io/pedsuite/reference/pedsuite-package.html","id":null,"dir":"Reference","previous_headings":"","what":"pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis — pedsuite-package","title":"pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis — pedsuite-package","text":"'pedsuite' collection packages pedigree analysis, covering applications forensic genetics, medical genetics . detailed presentation 'pedsuite' given book 'Pedigree Analysis R' (Vigeland, 2021, ISBN: 9780128244302).","code":""},{"path":[]},{"path":"https://magnusdv.github.io/pedsuite/reference/pedsuite-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"pedsuite: Easy Installation of the 'pedsuite' Packages for Pedigree Analysis — pedsuite-package","text":"Maintainer: Magnus Dehli Vigeland m.d.vigeland@medisin.uio.(ORCID) Authors: Thore Egeland thore.egeland@nmbu.(ORCID)","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-131","dir":"Changelog","previous_headings":"","what":"pedsuite 1.3.1","title":"pedsuite 1.3.1","text":"CRAN release: 2024-09-06 New package: pedFamilias Add several app homepages Minor code updates","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-120","dir":"Changelog","previous_headings":"","what":"pedsuite 1.2.0","title":"pedsuite 1.2.0","text":"CRAN release: 2023-06-26 Update Github Actions workflow Update pkgdown stuff Various minor improvements Add citation info","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-110","dir":"Changelog","previous_headings":"","what":"pedsuite 1.1.0","title":"pedsuite 1.1.0","text":"CRAN release: 2022-01-07 Include verbalisr core package Remove pedmut core package Fix CRAN note namespaces imported Minor README changes","code":""},{"path":"https://magnusdv.github.io/pedsuite/news/index.html","id":"pedsuite-104","dir":"Changelog","previous_headings":"","what":"pedsuite 1.0.4","title":"pedsuite 1.0.4","text":"CRAN release: 2021-06-21 Initial CRAN version","code":""}]