Skip to content

Commit

Permalink
first commit
Browse files Browse the repository at this point in the history
  • Loading branch information
@elswob
elswob committed Jul 8, 2015
0 parents commit 0872917
Show file tree
Hide file tree
Showing 22 changed files with 1,932 additions and 0 deletions.
2 changes: 2 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
^.*\.Rproj$
^\.Rproj\.user$
3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
.Rproj.user
.Rhistory
.RData
21 changes: 21 additions & 0 deletions BASAL.Rproj
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: knitr
LaTeX: pdfLaTeX

AutoAppendNewline: Yes
StripTrailingWhitespace: Yes

BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate,namespace,vignette
10 changes: 10 additions & 0 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
Package: BASAL
Type: Package
Title: What the Package Does (Title Case)
Version: 0.1
Date: 2015-07-08
Author: Who wrote it
Maintainer: Who to complain to <[email protected]>
Description: More about what it does (maybe more than one line)
License: What license is it under?
LazyData: TRUE
52 changes: 52 additions & 0 deletions Data/220arrays_nonUBCcommon+12normal_50g.txt

Large diffs are not rendered by default.

51 changes: 51 additions & 0 deletions Data/mediansPerDataset_v2.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
arrayTrain_postMeanCollapse htp1.5_WU_update commercial_4x44k_postMeanCollapse_WashU_v2 commercial_1x44k_postMeanCollapse_WashU
ACTR3B -0.5155 1.833329153 -0.242846154 -0.187
ANLN -2.479 -1.155718884 -2.51515 -0.927
BAG1 -0.1115 -1.497888263 -0.079864865 -0.1665
BCL2 0.622 2.487484419 1.07725 0.237
BIRC5 -1.822 -0.283588588 -1.788589744 -0.2565
BLVRA 0.039 2.353384781 0.500923077 0.071
CCNB1 -2.237 0.37935647 -1.922225 -1.2715
CCNE1 -1.0145 0.651351044 -1.159175 -0.445
CDC20 -1.4325 -0.839824418 -2.337333333 -1.3615
CDC6 -2.3195 0.71656509 -2.4434 -1.606
CDCA1 -2.038 1.638392758 -2.109948718 -1.417
CDH3 0.632 1.366044601 0.1884861 0.532
CENPF -1.879 -0.962983198 -2.009641026 -1.3315
CEP55 -2.04 -0.371643412 -2.079578947 -0.964
CXXC5 -0.0505 1.927138533 -0.368105263 -0.3395
EGFR -0.045 -0.40895264 -1.61425 -0.876
ERBB2 2.0265 3.373980383 2.213675 1.301
ESR1 1.1185 2.916796808 0.851794872 0.5205
EXO1 -2.0815 -0.436104334 -1.7515 -1.345
FGFR4 -1.5571 -0.09021586 -1.17074359 -0.306
FOXA1 1.7755 2.004403583 0.756825 1.38
FOXC1 -0.45 1.42887446 -0.884275 -0.329
GPR160 0.383 5.666021198 0.879894737 0.3855
GRB7 0.772 0.37176255 0.727868421 0.205
KIF2C -1.831 -0.978650592 -2.0756 -1.2595
KNTC2 -2.0635 -0.475240357 -1.828 -1.718
KRT14 0.2785 1.238253748 -0.39615 -0.0455
KRT17 -0.459 0.246015736 -1.164825 -0.9995
KRT5 -0.6805 2.234875966 -1.19165 -0.8565
MAPT 0 1.148998514 0.4418 0.104
MDM2 0.2405 6.503630597 -0.272666667 -0.1375
MELK -1.9175 -0.787196863 -1.9323 -1.3565
MIA -0.715 1.991145772 -1.043333333 -0.6455
MKI67 -1.6965 -0.757719431 -2.965948718 -0.733
MLPH 0.8465 1.963068745 -0.066131579 0.101
MMP11 3.289 6.967634333 2.892685714 2.0165
MYBL2 -1.9115 -1.981576466 -1.603775 -0.397
MYC -1.617 0.426752831 -2.335 -1.8795
NAT1 1.081 0.827508907 3.105475 0.8945
ORC6L -2.4095 -1.400635704 -2.7957 0.4965
PGR 0.648444444 1.030792302 -1.177483871 -0.905
PHGDH -1.9655 -0.949022832 -1.90485 -1.387
PTTG1 -1.8915 -1.064268952 -1.686974359 -1.224
RRM2 -2.567 -0.803239531 -2.46925641 -0.308
SFRP1 -0.526 2.754784698 -1.08525 -0.0475
SLC39A6 -0.8825 -0.557500599 -0.477 -0.942
TMEM45B -1.3705 1.998777205 -1.57915 -0.622
TYMS -2.795 0.344801316 -2.783052632 -1.963
UBE2C -1.089 -0.743295045 -2.214897436 -1.121
UBE2T -1.723 -0.152282102 -1.557513514 -1.029
51 changes: 51 additions & 0 deletions Data/pam50_annotation.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
pcrID UniGene EntrezGene GeneName InProliferation
ACTR3B Hs.647117 57180 ACTR3B N
ANLN Hs.62180 54443 ANLN N
BAG1 Hs.377484 573 BAG1 N
BCL2 Hs.150749 596 BCL2 N
BIRC5 Hs.514527 332 BIRC5 Y
BLVRA Hs.488143 644 BLVRA N
CCNB1 Hs.23960 891 CCNB1 Y
CCNE1 Hs.244723 898 CCNE1 N
CDC20 Hs.524947 991 CDC20 Y
CDC6 Hs.405958 990 CDC6 N
CDCA1 Hs.651950 83540 NUF2 Y
CDH3 Hs.461074 1001 CDH3 N
CENPF Hs.497741 1063 CENPF N
CEP55 Hs.14559 55165 CEP55 Y
CXXC5 Hs.189119 51523 CXXC5 N
EGFR Hs.488293 1956 EGFR N
ERBB2 Hs.446352 2064 ERBB2 N
ESR1 Hs.208124 2099 ESR1 N
EXO1 Hs.498248 9156 EXO1 N
FGFR4 Hs.165950 2264 FGFR4 N
FOXA1 Hs.163484 3169 FOXA1 N
FOXC1 Hs.348883 2296 FOXC1 N
GPR160 Hs.231320 26996 GPR160 N
GRB7 Hs.86859 2886 GRB7 N
KIF2C Hs.69360 11004 KIF2C N
KNTC2 Hs.414407 10403 NDC80 Y
KRT14 Hs.654380 3861 KRT14 N
KRT17 Hs.2785 3872 KRT17 N
KRT5 Hs.694210 3852 KRT5 N
MAPT Hs.101174 4137 MAPT N
MDM2 Hs.567303 4193 MDM2 N
MELK Hs.184339 9833 MELK N
MIA Hs.646364 8190 MIA N
MKI67 Hs.80976 4288 MKI67 Y
MLPH Hs.102406 79083 MLPH N
MMP11 Hs.143751 4320 MMP11 N
MYBL2 Hs.179718 4605 MYBL2 N
MYC Hs.202453 4609 MYC N
NAT1 Hs.591847 9 NAT1 N
ORC6L Hs.49760 23594 ORC6L N
PGR Hs.368072 5241 PGR N
PHGDH Hs.487296 26227 PHGDH N
PTTG1 Hs.350966 9232 PTTG1 Y
RRM2 Hs.226390 6241 RRM2 Y
SFRP1 Hs.695991 6422 SFRP1 N
SLC39A6 Hs.79136 25800 SLC39A6 N
TMEM45B Hs.504301 120224 TMEM45B N
TYMS Hs.592338 7298 TYMS Y
UBE2C Hs.93002 11065 UBE2C Y
UBE2T Hs.5199 29089 UBE2T N
51 changes: 51 additions & 0 deletions Data/pam50_centroids.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
Basal Her2 LumA LumB Normal
ACTR3B 0.71833189105221 -0.481665674726704 0.0099810704381048 -0.190551327982217 0.465722870515964
ANLN 0.537372300595531 0.26693160932886 -0.57924571615828 0.0988041789187431 -0.83693959305506
BAG1 -0.574506867003171 -0.476072868053812 0.758221161127353 -0.405458622327578 0.316552972849696
BCL2 -0.118760430362242 -0.157913959232179 0.287487439627067 -0.44133949784535 0.533978871455655
BIRC5 0.300488641307438 0.405733099101299 -0.881434366334594 0.603850776734403 -0.876636423925443
BLVRA -0.642677513396256 0.335336040994047 0.0420420167875037 0.691204961687021 -0.163412811613957
CCNB1 0.191208143233350 0.135476651890144 -0.491662113750233 0.503176357566503 -0.545269311937199
CCNE1 0.5602710279181 0.0668722320900592 -0.430291227412725 -0.016661429525915 -0.255476058116241
CDC20 0.399695241707236 0.00835552010412316 -0.469044010265104 -0.0704124657384466 -0.0455048098566988
CDC6 0.159418279239843 0.589006820321944 -0.61282430546711 0.510895969130001 -0.595752175354644
CDCA1 0.472400167554248 -0.0238192070320764 -0.712520818851019 0.589626882663298 -0.370533364608738
CDH3 0.508362012467715 0.210889691612697 -0.513649344383634 -1.41913443744317 0.757920623508959
CENPF 0.482976287851816 -0.0292661598656275 -0.54374023405061 0.278228556393300 -0.0705830752611994
CEP55 0.567748893765426 0.276381021673186 -0.746721735125358 0.460015762468336 -1.16237418628659
CXXC5 -0.92038581344894 -0.241550612126531 0.467411570831134 0.321335019875456 0.0509014360369965
EGFR -0.0304168492933523 -0.0963826205261192 0.00916296285683097 -0.412401259011741 0.341637082320563
ERBB2 -0.808353979685898 1.75984423053252 0.608191264034737 0.159651873930408 -0.870238456252032
ESR1 -2.74651308572764 -1.51311125337343 2.16141188167927 1.60589991409782 -0.418282349385733
EXO1 0.42809035571695 0.0492971938541269 -0.567474505364458 0.141241281899209 -0.4507805368292
FGFR4 -0.271238025272568 0.821778152444019 0.170811924512710 -0.247036037777853 0.857472776645833
FOXA1 -2.62694672123675 0.0228271511969584 1.0174574205457 0.360757794789733 -0.782812106272943
FOXC1 1.49045147226633 -0.947174191636912 -0.174957960004945 -1.56485496402643 1.11154786423416
GPR160 -1.05497467201534 0.583194826166968 0.685489972807875 0.714407601174597 -0.423568467196315
GRB7 -0.276128585792610 1.03065778049362 0.0415689860888212 0.0877508871181497 0.241710990681836
KIF2C 0.203572580112815 -0.165102048401172 -0.505394668119272 -0.18289071282855 -0.390014483980550
KNTC2 0.600356166736404 0.0425467918407693 -0.58822098932071 0.386706843524287 -1.06962886016236
KRT14 0.0968267225951578 -0.443646142118489 0.368375943286720 -0.639446965945955 1.73568631016155
KRT17 0.482565528200505 -0.337837101113602 0.0142098620606827 -1.46374293365444 1.75959843723177
KRT5 0.506640416426025 -0.42826177758168 0.215320067973960 -0.911607270494262 1.78511689525264
MAPT -0.42582927334418 -0.357506541134998 0.700622717588887 -0.19034057442467 0.117828498493485
MDM2 -0.251366205388229 -0.106728680574222 0.141957430453390 -0.133779036556646 0.274214010559593
MELK 0.523033872432266 0.198013114679137 -0.58208810796246 0.447934629706117 -0.743764675552645
MIA 1.57827636824347 -0.90489862111629 -0.165258584299697 -1.42292626721177 2.03885955577086
MKI67 0.476537447819512 0.065662359566943 -0.501871622444359 -0.145217867594777 -0.166004063281183
MLPH -0.339972458833524 -0.195228657981430 0.339304417889105 -0.456149914938842 0.750758364744867
MMP11 -0.556037671980059 0.5067587600346 -0.00625509011475386 0.33419930855919 -2.32698511905842
MYBL2 0.389893451959192 0.205263580428381 -0.84356993132705 0.467281990134531 -0.601704754297017
MYC 0.178763812453212 -1.04683283160474 -0.090830821420967 0.0152643973204342 1.02917620291809
NAT1 -0.936848945968056 -0.0899884918164858 2.92278679191125 0.470788041948480 -0.363273764184013
ORC6L 0.216304796525868 0.204402449297876 -0.352220666898442 0.110627650250106 -0.255879493250552
PGR -0.429133388609156 -0.279409915717406 0.445785002691586 -0.448839843849832 0.126011481678608
PHGDH 0.634518869785175 -0.186625862203220 -0.398682233972277 -1.03013931821750 0.66043775260378
PTTG1 0.264131894483995 0.055809894817994 -0.634468270258443 0.249725280730980 -0.549781259548456
RRM2 0.156204675747248 0.68272488919714 -0.950760200359295 0.350663839755693 -1.12105492950754
SFRP1 0.98798845910263 -1.04820266695367 0.131566363888596 -1.72045826151304 2.43628866770475
SLC39A6 -1.05112505157325 -0.695736456552694 2.06145907498356 1.65330302214459 0.116889693935195
TMEM45B -1.10945818050443 1.33063617180581 0.446242044594737 0.375688226418575 0.0362089142863473
TYMS 0.449800897311564 0.05294489694821 -0.644602075052837 0.492606521200551 -0.726989454321298
UBE2C 0.218534146535747 0.0610805976997803 -0.519818399226962 0.292799305558851 -0.40889468512475
UBE2T 0.389908898288675 0.28453681332228 -0.539259390713988 0.738952133209629 -0.952381005370445
1 change: 1 addition & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
exportPattern("^[[:alpha:]]+")
30 changes: 30 additions & 0 deletions R/bioclassifier_subtypeAssignment.R
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
###
# input variables for the subtype prediction script
###

bio_sub=function(){
paramDir<<- "./Data" # the location of unchanging files such as the function library and main program
#inputDir<- "" # the location of the data matrix, and where output will be located
#inputFile<- "" # the input data matrix as a tab delimited text file
#short<-"" # short name that will be used for output files

calibrationParameters<<- NA #the column of the "mediansPerDataset.txt" file to use for calibration;
#NA will force centering within the test set & -1 will not do any
#adjustment (when adjustment performed by used)

hasClinical<<-FALSE #may include tumor size as second row, with 'T' as the gene name,
#and encoded as binary (0 for size <= 2cm or 1 for size > 2cm)
#set this variable to FALSE if tumor size is not available

collapseMethod<-"mean" # can be mean or iqr (probe with max iqr is selected)
# typically, mean is preferred for long oligo and
# iqr is preferred for short oligo platforms


####
# run the assignment algorithm
####

#source(paste(paramDir,"subtypePrediction_functions.R",sep="/"))
#source(paste(paramDir,"subtypePrediction_distributed.R",sep="/"))
}
Loading

0 comments on commit 0872917

Please sign in to comment.