packageの依存性を管理するパッケージ
> install.packages("forecast", repos=c("http://rstudio.org/_packages", "http://cran.rstudio.com"))
Installing package into ‘C:/Users/ekaminuma/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘timeDate’, ‘tseries’, ‘fracdiff’, ‘RcppArmadillo’
---[p.255]----------------------------------------------------
Enriching RNA-seq data with GO terms
https://bioconductor.org/packages/devel/bioc/manuals/goseq/man/goseq.pdf
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
>
> biocLite("goseq")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.5.
Installing package(s) ‘goseq’
also installing the dependency ‘geneLenDataBase
> library(goseq)
> library(edgeR)
> supportedGenomes()
db species date
1 hg38 Human Dec. 2013
2 hg19 Human Feb. 2009
3 hg18 Human Mar. 2006
4 hg17 Human May 2004
5 hg16 Human Jul. 2003
6 vicPac2 Alpaca Mar. 2013
7 vicPac1 Alpaca Jul. 2008
8 dasNov3 Armadillo Dec. 2011
9 papHam1 Baboon Nov. 2008
10 panPan1 Bonobo May 2012
11 aptMan1 Brown kiwi Jun. 2015
12 otoGar3 Bushbaby Mar. 2011
13 papAnu2 Bushbaby Mar. 2012
14 felCat8 Cat Nov. 2014
15 felCat5 Cat Sep. 2011
16 felCat4 Cat Dec. 2008
17 felCat3 Cat Mar. 2006
18 panTro4 Chimp Feb. 2011
19 panTro3 Chimp Oct. 2010
20 panTro2 Chimp Mar. 2006
21 panTro1 Chimp Nov. 2003
22 criGri1 Chinese hamster Jul. 2013
23 bosTau8 Cow Jun. 2014
24 bosTau7 Cow Oct. 2011
25 bosTau6 Cow Nov. 2009
26 bosTau4 Cow Oct. 2007
27 bosTau3 Cow Aug. 2006
28 bosTau2 Cow Mar. 2005
29 macFas5 Crab-eating macaque Jun. 2013
30 canFam3 Dog Sep. 2011
31 canFam2 Dog May 2005
32 canFam1 Dog Jul. 2004
33 turTru2 Dolphin Oct. 2011
34 loxAfr3 Elephant Jul. 2009
35 musFur1 Ferret Apr. 2011
36 nomLeu3 Gibbon Oct. 2012
37 nomLeu2 Gibbon Jun. 2011
38 nomLeu1 Gibbon Jan. 2010
39 gorGor4 Gorilla Dec 2014
40 gorGor3 Gorilla May 2011
41 cavPor3 Guinea pig Feb. 2008
42 eriEur2 Hedgehog May 2012
43 eriEur1 Hedgehog Jun. 2006
44 equCab2 Horse Sep. 2007
45 equCab1 Horse Jan. 2007
46 dipOrd1 Kangaroo rat Jul. 2008
47 triMan1 Manatee Oct. 2011
48 calJac3 Marmoset Mar. 2009
49 calJac1 Marmoset Jun. 2007
50 pteVam1 Megabat Jul. 2008
51 myoLuc2 Microbat Jul. 2010
52 balAcu1 Minke whale Oct. 2013
53 mm10 Mouse Dec. 2011
54 mm9 Mouse Jul. 2007
55 mm8 Mouse Feb. 2006
56 mm7 Mouse Aug. 2005
57 micMur2 Mouse lemur May 2015
58 micMur1 Mouse lemur Jul. 2007
59 hetGla2 Naked mole-rat Jan. 2012
60 hetGla1 Naked mole-rat Jul. 2011
61 monDom5 Opossum Oct. 2006
62 monDom4 Opossum Jan. 2006
63 monDom1 Opossum Oct. 2004
64 ponAbe2 Orangutan Jul. 2007
65 ailMel1 Panda Dec. 2009
66 susScr3 Pig Aug. 2011
67 susScr2 Pig Nov. 2009
68 ochPri3 Pika May 2012
69 ochPri2 Pika Jul. 2008
70 ornAna2 Platypus Feb. 2007
71 ornAna1 Platypus Mar. 2007
72 oryCun2 Rabbit Apr. 2009
73 rn6 Rat Jul. 2014
74 rn5 Rat Mar. 2012
75 rn4 Rat Nov. 2004
76 rn3 Rat Jun. 2003
77 rheMac8 Rhesus Nov. 2015
78 rheMac3 Rhesus Oct. 2010
79 rheMac2 Rhesus Jan. 2006
80 proCap1 Rock hyrax Jul. 2008
81 oviAri3 Sheep Aug. 2012
82 oviAri1 Sheep Feb. 2010
83 sorAra2 Shrew Aug. 2008
84 sorAra1 Shrew Jun. 2006
85 choHof1 Sloth Jul. 2008
86 speTri2 Squirrel Nov. 2011
87 saiBol1 Squirrel monkey Oct. 2011
88 tarSyr2 Tarsier Sep. 2013
89 tarSyr1 Tarsier Aug. 2008
90 sarHar1 Tasmanian devil Feb. 2011
91 echTel2 Tenrec Nov. 2012
92 echTel1 Tenrec Jul. 2005
93 tupBel1 Tree shrew Dec. 2006
94 macEug2 Wallaby Sep. 2009
95 cerSim1 White rhinoceros May 2012
96 allMis1 American alligator Aug. 2012
97 gadMor1 Atlantic cod May 2010
98 melUnd1 Budgerigar Sep. 2011
99 galGal4 Chicken Nov.\n2011
100 galGal3 Chicken May 2006
101 galGal2 Chicken Feb. 2004
102 latCha1 Coelacanth Aug. 2011
103 calMil1 Elephant shark Dec. 2013
104 fr3 Fugu Oct. 2011
105 fr2 Fugu Oct. 2004
106 fr1 Fugu Aug. 2002
107 petMar2 Lamprey Sep. 2010
108 petMar1 Lamprey Mar. 2007
109 anoCar2 Lizard May 2010
110 anoCar1 Lizard Feb. 2007
111 oryLat2 Medaka Oct. 2005
112 geoFor1 Medium ground finch Apr. 2012
113 oreNil2 Nile tilapia Jan. 2011
114 chrPic1 Painted turtle Dec. 2011
115 gasAcu1 Stickleback Feb. 2006
116 tetNig2 Tetraodon Mar. 2007
117 tetNig1 Tetraodon Feb. 2004
118 melGal1 Turkey Dec. 2009
119 xenTro7 X. tropicalis Sep. 2012
120 xenTro3 X. tropicalis Nov. 2009
121 xenTro2 X. tropicalis Aug. 2005
122 xenTro1 X. tropicalis Oct. 2004
123 taeGut2 Zebra finch Feb. 2013
124 taeGut1 Zebra finch Jul. 2008
125 danRer10 Zebrafish Sep. 2014
126 danRer7 Zebrafish Jul. 2010
127 danRer6 Zebrafish Dec. 2008
128 danRer5 Zebrafish Jul. 2007
129 danRer4 Zebrafish Mar. 2006
130 danRer3 Zebrafish May 2005
131 ci2 C. intestinalis Mar. 2005
132 ci1 C. intestinalis Dec. 2002
133 braFlo1 Lancelet Mar. 2006
134 strPur2 S. purpuratus Sep. 2006
135 strPur1 S. purpuratus Apr. 2005
136 apiMel2 A. mellifera Jan. 2005
137 apiMel1 A. mellifera Jul. 2004
138 anoGam1 A. gambiae Feb. 2003
139 droAna2 D. ananassae Aug. 2005
140 droAna1 D. ananassae Jul. 2004
141 droEre1 D. erecta Aug. 2005
142 droGri1 D. grimshawi Aug. 2005
143 dm6 D. melanogaster Aug. 2014
144 dm3 D. melanogaster Apr. 2006
145 dm2 D. melanogaster Apr. 2004
146 dm1 D. melanogaster Jan. 2003
147 droMoj2 D. mojavensis Aug. 2005
148 droMoj1 D. mojavensis Aug. 2004
149 droPer1 D. persimilis Oct. 2005
150 dp3 D. pseudoobscura Nov. 2004
151 dp2 D. pseudoobscura Aug. 2003
152 droSec1 D. sechellia Oct. 2005
153 droSim1 D. simulans Apr. 2005
154 droVir2 D. virilis Aug. 2005
155 droVir1 D. virilis Jul. 2004
156 droYak2 D. yakuba Nov. 2005
157 droYak1 D. yakuba Apr. 2004
158 caePb2 C. brenneri Feb. 2008
159 caePb1 C. brenneri Jan. 2007
160 cb3 C. briggsae Jan. 2007
161 cb1 C. briggsae Jul. 2002
162 ce11 C. elegans Feb. 2013
163 ce10 C. elegans Oct. 2010
164 ce6 C. elegans May 2008
165 ce4 C. elegans Jan. 2007
166 ce2 C. elegans Mar. 2004
167 caeJap1 C. japonica Mar. 2008
168 caeRem3 C. remanei May 2007
169 caeRem2 C. remanei Mar. 2006
170 priPac1 P. pacificus Feb. 2007
171 aplCal1 Sea Hare Sep. 2008
172 sacCer3 Yeast April 2011
173 sacCer2 Yeast June 2008
174 sacCer1 Yeast Oct. 2003
175 eboVir3 Ebola Virus June 2014
name
1 Genome Reference Consortium GRCh38
2 Genome Reference Consortium GRCh37
3 NCBI Build 36.1
4 NCBI Build 35
5 NCBI Build 34
6 Broad Institute Vicugna_pacos-2.0.1
7 Broad Institute VicPac1.0
8 Broad Institute DasNov3
9 Baylor College of Medicine HGSC Pham_1.0
10 Max-Planck Institute panpan1
11 Max-Plank Institute for Evolutionary Anthropology AptMant0
12 Broad Institute OtoGar3
13 Baylor College of Medicine Panu_2.0
14 ICGSC Felis_catus_8.0
15 ICGSC Felis_catus-6.2
16 NHGRI catChrV17e
17 Broad Institute Release 3
18 CGSC Build 2.1.4
19 CGSC Build 2.1.3
20 CGSC Build 2.1
21 CGSC Build 1.1
22 Beijing Genomics Institution-Shenzhen C_griseus_v1.0
23 University of Maryland v3.1.1
24 Baylor College of Medicine HGSC Btau_4.6.1
25 University of Maryland v3.1
26 Baylor College of Medicine HGSC Btau_4.0
27 Baylor College of Medicine HGSC Btau_3.1
28 Baylor College of Medicine HGSC Btau_2.0
29 Washington University Macaca_fascicularis_5.0
30 Broad Institute v3.1
31 Broad Institute v2.0
32 Broad Institute v1.0
33 Baylor College of Medicine Ttru_1.4
34 Broad Institute LoxAfr3
35 Ferret Genome Sequencing Consortium MusPutFur1.0
36 Gibbon Genome Sequencing Consortium Nleu3.0
37 Gibbon Genome Sequencing Consortium Nleu1.1
38 Gibbon Genome Sequencing Consortium Nleu1.0
39 Wellcome Trust Sanger Institute gorGor4
40 Wellcome Trust Sanger Institute gorGor3.1
41 Broad Institute cavPor3
42 Broad Institute EriEur2.0
43 Broad Institute Draft_v1
44 Broad Institute EquCab2
45 Broad Institute EquCab1
46 Baylor/Broad Institute DipOrd1.0
47 Broad Institute TriManLat1.0
48 WUSTL Callithrix_jacchus-v3.2
49 WUSTL Callithrix_jacchus-v2.0.2
50 Broad Institute Ptevap1.0
51 Broad Institute MyoLuc2.0
52 KORDI BalAcu1.0
53 Genome Reference Consortium GRCm38
54 NCBI Build 37
55 NCBI Build 36
56 NCBI Build 35
57 Baylor/Broad Institute Mmur_2.0
58 Broad Institute MicMur1.0
59 Broad Institute HetGla_female_1.0
60 Beijing Genomics Institute HetGla_1.0
61 Broad Institute release MonDom5
62 Broad Institute release MonDom4
63 Broad Institute release MonDom1
64 WUSTL Pongo_albelii-2.0.2
65 BGI-Shenzhen AilMel 1.0
66 Swine Genome Sequencing Consortium Sscrofa10.2
67 Swine Genome Sequencing Consortium Sscrofa9.2
68 Broad Institute OchPri3.0
69 Broad Institute OchPri2
70 WUSTL v5.0.1
71 WUSTL v5.0.1
72 Broad Institute release OryCun2
73 RGSC Rnor_6.0
74 RGSC Rnor_5.0
75 Baylor College of Medicine HGSC v3.4
76 Baylor College of Medicine HGSC v3.1
77 Baylor College of Medicine HGSC Mmul_8.0.1
78 Beijing Genomics Institute CR_1.0
79 Baylor College of Medicine HGSC v1.0 Mmul_051212
80 Baylor College of Medicine HGSC Procap1.0
81 ISGC Oar_v3.1
82 ISGC Ovis aries 1.0
83 Broad Institute SorAra2.0
84 Broad Institute SorAra1.0
85 Broad Institute ChoHof1.0
86 Broad Institute SpeTri2.0
87 Broad Institute SaiBol1.0
88 WashU Tarsius_syrichta-2.0.1
89 WUSTL/Broad Institute Tarsyr1.0
90 Wellcome Trust Sanger Institute Devil_refv7.0
91 Broad Institute EchTel2.0
92 Broad Institute echTel1
93 Broad Institute Tupbel1.0
94 Tammar Wallaby Genome Sequencing Consortium Meug_1.1
95 Broad Institute CerSimSim1.0
96 Int. Crocodilian Genomes Working Group allMis0.2
97 Genofisk GadMor_May2010
98 WUSTL v6.3
99 ICGC Gallus-gallus-4.0
100 WUSTL Gallus-gallus-2.1
101 WUSTL Gallus-gallus-1.0
102 Broad Institute LatCha1
103 IMCB Callorhinchus_milli_6.1.3
104 JGI v5.0
105 JGI v4.0
106 JGI v3.0
107 WUGSC 7.0
108 WUSTL v3.0
109 Broad Institute AnoCar2
110 Broad Institute AnoCar1
111 NIG v1.0
112 BGI GeoFor_1.0 / NCBI 13302
113 Broad Institute Release OreNil1.1
114 IPTGSC Chrysemys_picta_bellii-3.0.1
115 Broad Institute Release 1.0
116 Genoscope v7
117 Genoscope v7
118 Turkey Genome Consortium v2.01
119 JGI v.7.0
120 JGI v.4.2
121 JGI v.4.1
122 JGI v.3.0
123 WashU taeGut324
124 WUSTL v3.2.4
125 Genome Reference Consortium GRCz10
126 Sanger Institute Zv9
127 Sanger Institute Zv8
128 Sanger Institute Zv7
129 Sanger Institute Zv6
130 Sanger Institute Zv5
131 JGI v2.0
132 JGI v1.0
133 JGI v1.0
134 Baylor College of Medicine HGSC v. Spur 2.1
135 Baylor College of Medicine HGSC v. Spur_0.5
136 Baylor College of Medicine HGSC v.Amel_2.0
137 Baylor College of Medicine HGSC v.Amel_1.2
138 IAGP v.MOZ2
139 Agencourt Arachne release
140 TIGR Celera release
141 Agencourt Arachne release
142 Agencourt Arachne release
143 BDGP Release 6 + ISO1 MT
144 BDGP Release 5
145 BDGP Release 4
146 BDGP Release 3
147 Agencourt Arachne release
148 Agencourt Arachne release
149 Broad Institute release
150 Flybase Release 1.0
151 Baylor College of Medicine HGSC Freeze 1
152 Broad Institute Release 1.0
153 WUSTL Release 1.0
154 Agencourt Arachne release
155 Agencourt Arachne release
156 WUSTL Release 2.0
157 WUSTL Release 1.0
158 WUSTL 6.0.1
159 WUSTL 4.0
160 WUSTL Cb3
161 WormBase v. cb25.agp8
162 C. elegans Sequencing Consortium WBcel235
163 WormBase v. WS220
164 WormBase v. WS190
165 WormBase v. WS170
166 WormBase v. WS120
167 WUSTL 3.0.2
168 WUSTL 15.0.1
169 WUSTL 1.0
170 WUSTL 5.0
171 Broad Release Aplcal2.0
172 SGD April 2011 sequence
173 SGD June 2008 sequence
174 SGD 1 Oct 2003 sequence
175 Sierra Leone 2014 (G3683/KM034562.1)
:
<続く>
> dat1<-read.table("Li_sum.txt",header=TRUE,stringsAsFactors=FALSE,row.names=1)
>
> head(dat1)
lane1 lane2 lane3 lane4 lane5 lane6 lane8
ENSG00000215688 0 0 0 0 0 0 0
ENSG00000215689 0 0 0 0 0 0 0
ENSG00000220823 0 0 0 0 0 0 0
ENSG00000242499 0 0 0 0 0 0 0
ENSG00000224938 0 0 0 0 0 0 0
ENSG00000239242 0 0 0 0 0 0 0
> mytr <- factor(rep(c("Control","Treatment"),times=c(4,3)) )
> mytr
[1] Control Control Control Control Treatment Treatment Treatment
Levels: Control Treatment
> myDG<-DGEList(dat1,lib.size=colSums(dat1),group=mytr)
> myDG
An object of class "DGEList"
$counts
lane1 lane2 lane3 lane4 lane5 lane6 lane8
ENSG00000215688 0 0 0 0 0 0 0
ENSG00000215689 0 0 0 0 0 0 0
ENSG00000220823 0 0 0 0 0 0 0
ENSG00000242499 0 0 0 0 0 0 0
ENSG00000224938 0 0 0 0 0 0 0
49501 more rows ...
$samples
group lib.size norm.factors
lane1 Control 1178832 1
lane2 Control 1384945 1
lane3 Control 1716355 1
lane4 Control 1767927 1
lane5 Treatment 2127868 1
lane6 Treatment 2142158 1
lane8 Treatment 816171 1
> disp1<-estimateCommonDisp(myDG)
> disp1
An object of class "DGEList"
$counts
lane1 lane2 lane3 lane4 lane5 lane6 lane8
ENSG00000215688 0 0 0 0 0 0 0
ENSG00000215689 0 0 0 0 0 0 0
ENSG00000220823 0 0 0 0 0 0 0
ENSG00000242499 0 0 0 0 0 0 0
ENSG00000224938 0 0 0 0 0 0 0
49501 more rows ...
$samples
group lib.size norm.factors
lane1 Control 1178832 1
lane2 Control 1384945 1
lane3 Control 1716355 1
lane4 Control 1767927 1
lane5 Treatment 2127868 1
lane6 Treatment 2142158 1
lane8 Treatment 816171 1
$common.dispersion
[1] 0.05688364
$pseudo.counts
:
> mytest<- exactTest(disp1)
> mytest
An object of class "DGEExact"
$table
logFC logCPM PValue
ENSG00000215688 0 0.330418 1
ENSG00000215689 0 0.330418 1
ENSG00000220823 0 0.330418 1
ENSG00000242499 0 0.330418 1
ENSG00000224938 0 0.330418 1
49501 more rows ...
$comparison
[1] "Control" "Treatment"
$genes
NULL
> mytag1<-as.integer(p.adjust(mytest$table$Pvalue[mytest$table$logFC!=0],method="BH")<0.05)
>
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade
for help
> biocLite("geneLenDataBase")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.5.
Installing package(s) ‘geneLenDataBase’
---[p.258]----------------
田中さん担当分
The KEGG enrichment of sequence data
---[p.260]------------------------------------------------------
Analyzing methylation data
> biocLite("methyAnalysis")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.5.
Installing package(s) ‘methyAnalysis’
> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
> library(methyAnalysis)
要求されたパッケージ grid をロード中です
要求されたパッケージ BiocGenerics をロード中です
> data(exampleMethyGenoSet)
> summary(exampleMethyGenoSet)
Length Class Mode
1 MethyGenoSet S4
> slotNames(exampleMethyGenoSet)
[1] "history" "locData" "assayData"
[4] "phenoData" "featureData" "experimentData"
[7] "annotation" "protocolData" ".__classVersion__"
> head(locData(exampleMethyGenoSet)
+ )
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
cg17035109 chr21 [10882029, 10882029] *
cg06187584 chr21 [10883548, 10883548] *
cg12459059 chr21 [10884748, 10884748] *
cg25450479 chr21 [10884967, 10884967] *
cg23347501 chr21 [10884969, 10884969] *
cg03661019 chr21 [10885409, 10885409] *
-------
seqinfo: 1 sequence from hg19 genome; no seqlengths
> dim(exprs(exampleMethyGenoSet))
[1] 4243 8
>
> pData(exampleMethyGenoSet)
SampleType
Sample1 Type1
Sample2 Type1
Sample3 Type1
Sample4 Type1
Sample5 Type2
Sample6 Type2
Sample7 Type2
Sample8 Type2
警告メッセージ:
'pData' is deprecated.
Use 'colData' instead.
See help("Deprecated")
> str(exampleMethyGenoSet)
Formal class 'MethyGenoSet' [package "methyAnalysis"] with 9 slots
..@ history :'data.frame': 8 obs. of 4 variables:
.. ..$ submitted : chr [1:8] "2011-03-30 20:52:40" "2011-03-30 21:19:32" "2011-04-11 15:27:15" "2011-04-11 15:30:45" ...
.. ..$ finished : chr [1:8] "2011-03-30 21:19:32" "2011-03-30 21:21:22" "2011-04-11 15:29:27" "2011-04-11 15:32:36" ...
> sm <- smoothMethyData(exampleMethyGenoSet,winSize=200)
Smoothing Chromosome chr21 ...
> sm
MethyGenoSet (storageMode: lockedEnvironment)
assayData: 4243 features, 8 samples
element names: detection, exprs, methylated, unmethylated
protocolData: none
phenoData
sampleNames: Sample1 Sample2 ... Sample8 (8 total)
varLabels: SampleType
varMetadata: labelDescription
featureData
featureNames: cg17035109 cg06187584 ... cg08821909 (4243
total)
fvarLabels: ID
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: IlluminaHumanMethylation450k.db
Feature Locations:
GRanges object with 4243 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
cg17035109 chr21 [10882029, 10882029] *
cg06187584 chr21 [10883548, 10883548] *
cg12459059 chr21 [10884748, 10884748] *
cg25450479 chr21 [10884967, 10884967] *
cg23347501 chr21 [10884969, 10884969] *
... ... ... ...
cg14365143 chr21 [48088046, 48088046] *
cg22544673 chr21 [48088150, 48088150] *
cg02984790 chr21 [48090128, 48090128] *
cg07468397 chr21 [48090508, 48090508] *
cg08821909 chr21 [48091011, 48091011] *
-------
seqinfo: 1 sequence from hg19 genome; no seqlengths
> attr(sm,'windowSize')
[1] 200
> cond <- pData(exampleMethyGenoSet)$SampleType
警告メッセージ:
'pData' is deprecated.
Use 'colData' instead.
See help("Deprecated")
>
> cond <- colData(exampleMethyGenoSet)$SampleType
>
> myDMR <- detectDMR.slideWin(exampleMethyGenoSet,sampleType=cond)
Smoothing Chromosome chr21 ...
>
> head(myDMR)
GRanges object with 6 ranges and 11 metadata columns:
seqnames ranges strand | PROBEID
<Rle> <IRanges> <Rle> | <factor>
cg17035109 chr21 [10882029, 10882029] * | cg17035109
cg06187584 chr21 [10883548, 10883548] * | cg06187584
cg12459059 chr21 [10884748, 10884748] * | cg12459059
cg25450479 chr21 [10884967, 10884967] * | cg25450479
cg23347501 chr21 [10884969, 10884969] * | cg23347501
cg03661019 chr21 [10885409, 10885409] * | cg03661019
difference p.value p.adjust tscore
<numeric> <numeric> <numeric> <numeric>
cg17035109 -1.8411605 0.06276449 0.1888488 -2.2804091
cg06187584 -0.4566059 0.41601486 0.6149596 -0.8734252
cg12459059 -0.3591179 0.36542152 0.5627904 -0.9789270
cg25450479 -0.3591179 0.36542152 0.5627904 -0.9789270
cg23347501 -0.3591179 0.36542152 0.5627904 -0.9789270
cg03661019 -0.3532662 0.38065600 0.5782099 -0.9460314
startWinIndex endWinIndex startLocation endLocation
<numeric> <numeric> <integer> <integer>
cg17035109 1 1 10882029 10882029
cg06187584 2 2 10883548 10883548
cg12459059 3 5 10884748 10884969
cg25450479 3 5 10884748 10884969
cg23347501 3 5 10884748 10884969
cg03661019 6 6 10885409 10885409
mean_Type1 mean_Type2
<numeric> <numeric>
cg17035109 -2.4183775 -0.57721699
cg06187584 -2.2297567 -1.77315084
cg12459059 0.2594151 0.61853304
cg25450479 0.2594151 0.61853304
cg23347501 0.2594151 0.61853304
cg03661019 -0.4170363 -0.06377013
-------
seqinfo: 1 sequence from hg19 genome; no seqlengths
> SigDMR <- identifySigDMR(myDMR)
> dmr_ann <- annotateDMRInfo(SigDMR,'TxDb.Hsapiens.UCSC.hg19.knownGene')
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: GenomicFeatures
>
> export.DMRInfo(dmr_anno,savePrefix='testExample')
as.data.frame(DMRInfo.ann$sigDataInfo) でエラー:
引数 'x' の評価中にエラーが起きました (関数 'as.data.frame' に対するメソッドの選択時): エラー: オブジェクト 'dmr_anno' がありません
> export.DMRInfo(dmr_ann,savePrefix='test_dmr_ann')
PCのterminalでファイルを確認する。
na-no-MacBook-Pro:~ ekaminum$ ls -lt
total 32
-rw-r--r-- 1 ekaminum staff 2450 7 13 10:47 DMRInfo_test_dmr_ann_2016-07-13.csv
-rw-r--r-- 1 ekaminum staff 420 7 13 10:47 DMRInfo_test_dmr_ann_2016.07.13.bed
-rw-r--r-- 1 ekaminum staff 4491 7 13 10:47 DMRdata_test_dmr_ann_2016-07-13.csv
na-no-MacBook-Pro:~ ekaminum$ cat DMRInfo_test_dmr_ann_2016-07-13.csv
"CHROMOSOME","start","end","NumOfProbe","min_p.value","max_difference","min_p.adjust","max_tscore","mean_Type1","mean_Type2","Transcript","EntrezID","GeneSymbol","distance2TSS","nearestTx","PROMOTER"
"chr21",19191045,19191320,3,0.0001235924,-1.1907873545,0.007061388,-8.74702112,-4.02704733856667,-2.92264438366667,"uc002yko.4","54149","C21orf91",383,"uc002yko.4",FALSE
"chr21",34522588,34522588,1,0.000007677523,-1.2848047397,0.003093883,-14.182749104,-4.5115552816,-3.226750542,"uc002yra.4","728409","LINC01548",19953,"uc002yra.4",FALSE
"chr21",37851847,37851847,1,0.00009416121,-1.4922516167,0.006768435,-9.179626306,0.6201243857,2.112376002,"uc002yvl.1","23562","CLDN14",541,"uc002yvl.1",FALSE
na-no-MacBook-Pro:~ ekaminum$ cat DMRInfo_test_dmr_ann_2016.07.13.bed
chr21 19191044 19191320 . 0 .
chr21 34522587 34522588 . 0 .
chr21 37851846 37851847 . 0 .
chr21 38066046 38066047 . 0 .
chr21 38075598 38077042 . 0 .
chr21 38080974 38081193 . 0 .
chr21 39285678 39285679 . 0 .
chr21 39748802 39748803 . 0 .
na-no-MacBook-Pro:~ ekaminum$ cat DMRdata_test_dmr_ann_2016-07-13.csv
"CHROMOSOME","POSITION","PROBEID","difference","p.value","p.adjust","tscore","startWinIndex","endWinIndex","mean_Type1","mean_Type2","Transcript","EntrezID","GeneSymbol","distance2TSS","nearestTx","PROMOTER"
"chr21",19191096,"cg12430776",-1.07152346805949,0.000123592435561639,0.00706138813614358,-8.7470211196085,279,281,-4.09227128083324,-3.02074781277375,"uc002yko.4","54149","C21orf91",607,"uc002yko.4",FALSE
"chr21",34522588,"ch.21.33444458F",-1.28480473970052,7.6775226703329e-06,0.00309388312095657,-14.1827491036894,998,998,-4.51155528155554,-3.22675054185502,"uc002yra.4","728409","LINC01548",19953,"uc002yra.4",FALSE