------Bioconductorのインストール-----------------
※インストールに時間がかかりますので、早めに対応ください。
> source("http://bioconductor.org/biocLite.R")
Installing package into ‘C:/Users/ekaminuma/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/BiocInstaller_1.18.4.zip'
Content type 'application/zip' length 114483 bytes (111 KB)
downloaded 111 KB
package ‘BiocInstaller’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\ekaminuma\AppData\Local\Temp\RtmpAjY8mT\downloaded_packages
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’, ‘GenomeInfoDb’, ‘DBI’, ‘RSQLite’
略
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/AnnotationDbi_1.30.1.zip'
Content type 'application/zip' length 9453861 bytes (9.0 MB)
downloaded 9.0 MB
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
略
The downloaded binary packages are in
C:\Users\ekaminuma\AppData\Local\Temp\RtmpAjY8mT\downloaded_packages
Old packages: 'manipulate', 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]:
> biocLite(c("GenomicFeatures", "AnnotationDbi"))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘GenomicFeatures’, ‘AnnotationDbi’
also installing the dependencies ‘lambda.r’, ‘futile.options’, ‘futile.logger’, ‘snow’, ‘BiocParallel’, ‘bitops’, ‘zlibbioc’, ‘XML’, ‘Rsamtools’, ‘GenomicAlignments’, ‘GenomicRanges’, ‘RCurl’, ‘XVector’, ‘Biostrings’, ‘rtracklayer’, ‘biomaRt’
略
Old packages: 'manipulate', 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]:
n
> biocLite
function (pkgs = c("Biobase", "IRanges", "AnnotationDbi"), suppressUpdates = FALSE,
suppressAutoUpdate = FALSE, siteRepos = character(), ask = TRUE,
...)
{
if (missing(pkgs))
pkgs <- pkgs[!pkgs %in% rownames(installed.packages())]
if (!suppressAutoUpdate && !.isCurrentBiocInstaller()) {
on.exit(.updateBiocInstaller(pkgs, ask = ask, suppressUpdates = suppressUpdates,
siteRepos = siteRepos, ...))
}
else if ("BiocUpgrade" %in% pkgs) {
.biocUpgrade()
}
else {
.biocLiteInstall(pkgs, ask = ask, siteRepos = siteRepos,
suppressUpdates = suppressUpdates, ...)
}
}
<environment: namespace:BiocInstaller>
インストール先のダウンロードサイトを指定します。
> chooseBioCmirror()
HTTPS BioC mirror
1: 0-Bioconductor (World-wide) [https]
2: Germany (Dortmund) [https]
3: United Kingdom (Hinxton) [https]
4: Japan (Wako) [https]
5: China (Anhui) [https]
6: (HTTP mirrors)
Selection: 4
> chooseCRANmirror()
HTTPS CRAN mirror
1: 0-Cloud [https] 2: Austria [https]
3: Chile [https] 4: China (Beijing 4) [https]
5: China (Hefei) [https] 6: Colombia (Cali) [https]
7: France (Lyon 2) [https] 8: Germany (Munster) [https]
9: Iceland [https] 10: Russia (Moscow) [https]
11: Spain (A Coruna) [https] 12: Switzerland [https]
13: UK (Bristol) [https] 14: UK (Cambridge) [https]
15: USA (CA 1) [https] 16: USA (KS) [https]
17: USA (MI 1) [https] 18: USA (TN) [https]
19: USA (TX) [https] 20: USA (WA) [https]
21: (HTTP mirrors)
Selection:
メニューから項目を入力するか、0 を入力して終了して下さい
Selection: 0
-----[p.41]---------------------------------
BioconductorのAnnotation Data Packageを試す。
対象は、AffymetrixのHuman RNA解析Chip
＜参考：AffymetrixサイトでのRNA解析アレイの分類＞
3' IVT Expression Analysis | Gene Regulation Analysis | miRNA Analysis | Whole-Transcript Expression Analysis & Profiling
----------------------------------------------------------------------------
3'IVT Expression Analysis → Human Genome U133A Arrayのデータパッケージ「hgu133A」
参考：BioConductorのページ
> ?hgu133a.db ヘルプで確認
> biocLite("hgu133a.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘hgu133a.db’
also installing the dependency ‘org.Hs.eg.db’
installing the source packages ‘org.Hs.eg.db’, ‘hgu133a.db’
trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/org.Hs.eg.db_3.1.2.tar.gz'
Content type 'application/x-gzip' length 65439359 bytes (62.4 MB)
downloaded 62.4 MB
trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/hgu133a.db_3.1.3.tar.gz'
Content type 'application/x-gzip' length 903355 bytes (882 KB)
downloaded 882 KB
* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
*** arch - x64
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (org.Hs.eg.db)
* installing *source* package 'hgu133a.db' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
*** arch - x64
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (hgu133a.db)
The downloaded source packages are in
‘C:\Users\ekaminuma\AppData\Local\Temp\RtmpAjY8mT\downloaded_packages’
Old packages: 'manipulate', 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]:
n
> library("hgu133a.db")
要求されたパッケージ AnnotationDbi をロード中です
要求されたパッケージ stats4 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
要求されたパッケージ parallel をロード中です
次のパッケージを付け加えます: ‘BiocGenerics’
以下のオブジェクトは ‘package:parallel’ からマスクされています:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
略
アノテーションのうち、ENTRESIDのデータを利用する
> ls("package:hgu133a.db")
[1] "hgu133a" "hgu133a.db" "hgu133a_dbconn"
[4] "hgu133a_dbfile" "hgu133a_dbInfo" "hgu133a_dbschema"
[7] "hgu133aACCNUM" "hgu133aALIAS2PROBE" "hgu133aCHR"
[10] "hgu133aCHRLENGTHS" "hgu133aCHRLOC" "hgu133aCHRLOCEND"
[13] "hgu133aENSEMBL" "hgu133aENSEMBL2PROBE" "hgu133aENTREZID"
[16] "hgu133aENZYME" "hgu133aENZYME2PROBE" "hgu133aGENENAME"
[19] "hgu133aGO" "hgu133aGO2ALLPROBES" "hgu133aGO2PROBE"
[22] "hgu133aMAP" "hgu133aMAPCOUNTS" "hgu133aOMIM"
[25] "hgu133aORGANISM" "hgu133aORGPKG" "hgu133aPATH"
[28] "hgu133aPATH2PROBE" "hgu133aPFAM" "hgu133aPMID"
[31] "hgu133aPMID2PROBE" "hgu133aPROSITE" "hgu133aREFSEQ"
[34] "hgu133aSYMBOL" "hgu133aUNIGENE" "hgu133aUNIPROT"
> myMap<-hgu133aENTREZID MyMap変数に抽出
> myMap
ENTREZID map for chip hgu133a (object of class "ProbeAnnDbBimap")
>
> summary(myMap)
ENTREZID map for chip hgu133a (object of class "ProbeAnnDbBimap")
|
| Lkeyname: probe_id (Ltablename: probes)
| Lkeys: "1007_s_at", "1053_at", ... (total=22283/mapped=19846)
|
| Rkeyname: gene_id (Rtablename: genes)
| Rkeys: "1", "2", ... (total=56340/mapped=12434)
|
| direction: L --> R
> mapped_probes<-mappedkeys(myMap)
> summary(mapped_probes)
Length Class Mode
19846 character character
> MyEntrez <- as.list(myMap[mapped_probes[1:5]])
リスト変数に1-5番目までのprobe番号に対応するEntrezIDをまとめる
> MyEntrez EntrezID番号
$`1053_at`
[1] "5982"
$`117_at`
[1] "3310"
$`121_at`
[1] "7849"
$`1255_g_at`
[1] "2978"
$`1316_at`
[1] "7067"
> MyEntrez[1] listエントリ1番目データへのアクセス
$`1053_at`
[1] "5982"
> MyEntrez[[1]] listエントリ1番目データの中身へアクセス
[1] "5982"
> d1 <- c() 空の変数作成
> for (i in 1:3){ d1<- append(d1, MyEntrez[[i]]) }
appendを使ってd1に1～3までの値を入力
> d1
[1] "5982" "3310" "7849"
-----[p.42]---------------------------------
遺伝子シンボルからEntrezIDに変換する
> biocLite("org.Hs.eg.db")
BioC_mirror: https://bioconductor.riken.jp
Using Bioconductor version 3.1 (BiocInstaller 略
* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from p’
Old packages: 'manipulate', 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]:
n
> library(org.Hs.eg.db)
> myEIDs<-c("1","10","100","1000","37690")
> myEIDs
[1] "1" "10" "100" "1000" "37690"
>
> ls("package:org.Hs.eg.db")
[1] "org.Hs.eg" "org.Hs.eg.db"
[3] "org.Hs.eg_dbconn" "org.Hs.eg_dbfile"
[5] "org.Hs.eg_dbInfo" "org.Hs.eg_dbschema"
[7] "org.Hs.egACCNUM" "org.Hs.egACCNUM2EG"
[9] "org.Hs.egALIAS2EG" "org.Hs.egCHR"
[11] "org.Hs.egCHRLENGTHS" "org.Hs.egCHRLOC"
[13] "org.Hs.egCHRLOCEND" "org.Hs.egENSEMBL"
[15] "org.Hs.egENSEMBL2EG" "org.Hs.egENSEMBLPROT"
[17] "org.Hs.egENSEMBLPROT2EG" "org.Hs.egENSEMBLTRANS"
[19] "org.Hs.egENSEMBLTRANS2EG" "org.Hs.egENZYME"
[21] "org.Hs.egENZYME2EG" "org.Hs.egGENENAME"
[23] "org.Hs.egGO" "org.Hs.egGO2ALLEGS"
[25] "org.Hs.egGO2EG" "org.Hs.egMAP"
[27] "org.Hs.egMAP2EG" "org.Hs.egMAPCOUNTS"
[29] "org.Hs.egOMIM" "org.Hs.egOMIM2EG"
[31] "org.Hs.egORGANISM" "org.Hs.egPATH"
[33] "org.Hs.egPATH2EG" "org.Hs.egPFAM"
[35] "org.Hs.egPMID" "org.Hs.egPMID2EG"
[37] "org.Hs.egPROSITE" "org.Hs.egREFSEQ"
[39] "org.Hs.egREFSEQ2EG" "org.Hs.egSYMBOL"
[41] "org.Hs.egSYMBOL2EG" "org.Hs.egUCSCKG"
[43] "org.Hs.egUNIGENE" "org.Hs.egUNIGENE2EG"
[45] "org.Hs.egUNIPROT"
> mySymbols<-mget(myEIDs,org.Hs.egSYMBOL,ifnotfound=NA)
> mySymbols
$`1`
[1] "A1BG"
$`10`
[1] "NAT2"
$`100`
[1] "ADA"
$`1000`
[1] "CDH2"
$`37690`
[1] NA
> y<-mySymbols[!is.na(mySymbols)]
> y
1 10 100 1000
"A1BG" "NAT2" "ADA" "CDH2"
>
> myEIDs<-mget(y,org.Hs.egSYMBOL2EG,ifnotfound=NA) ※本と違うので注意
> myEIDs
$A1BG
[1] "1"
$NAT2
[1] "10"
$ADA
[1] "100"
$CDH2
[1] "1000"
----------[p.44]--------------------------------------------------------------------------
Pathwayデータベース「KEGG」データを使う
KEGG=パスウェイデータベースhttp://www.genome.jp/kegg/
KEGG API パスウェイで見たい生物種の遺伝子(EC番号)のみ表示できるhttps://www.google.co.jp/search?q=KEGG+API&hl=ja&source=lnms&tbm=isch&sa=X&ved=0CAgQ_AUoAWoVChMIz-fmgOusyAIVYeKmCh0u_AlN&biw=1008&bih=632
> biocLite("KEGG.db")
BioC_mirror: https://bioconductor.riken.jp
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘KEGG.db’
installing the source package ‘KEGG.db’
trying URL 'https://bioconductor.riken.jp/packages/3.1/data/annotation/src/contrib/KEGG.db_3.1.2.tar.gz'
Content type 'application/x-gzip' length 1973395 bytes (1.9 MB)
downloaded 1.9 MB
* installing *source* package 'KEGG.db' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
*** arch - x64
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (KEGG.db)
The downloaded source packages are in
‘C:\Users\ekaminuma\AppData\Local\Temp\RtmpAjY8mT\downloaded_packages’
Old packages: 'manipulate', 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]:
n
> library(KEGG.db)
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most recent
update was produced. This package should now be considered deprecated
and future versions of Bioconductor may not have it available. Users
who want more current data are encouraged to look at the KEGGREST or
reactome.db packages
> ?KEGG.db
> ls("package:KEGG.db")
[1] "KEGG" "KEGG_dbconn" "KEGG_dbfile" "KEGG_dbInfo"
[5] "KEGG_dbschema" "KEGGENZYMEID2GO" "KEGGEXTID2PATHID" "KEGGGO2ENZYMEID"
[9] "KEGGMAPCOUNTS" "KEGGPATHID2EXTID" "KEGGPATHID2NAME" "KEGGPATHNAME2ID"
> myEID <- unlist(mget(y, org.Hs.egSYMBOL2EG, ifnotfound=NA))
> myEID<-as.character(myEID)> myEID
[1] "1" "10" "100" "1000"
> kegg<-mget(myEID,KEGGEXTID2PATHID,ifnotfound=list(NA))
＝＞Entrez(Gene)IDからKEGG PathwayIDにマップするオブジェクト
> kegg
$`1`
[1] NA
$`10`
[1] "hsa00232" "hsa00983" "hsa01100"
$`100`
[1] "hsa00230" "hsa01100" "hsa05340"
$`1000`
[1] "hsa04514" "hsa05412"
-----------------------------------------------
KEGGのPathwayID番号からPathway名に変換
> kegg[[2]]
[1] "hsa00232" "hsa00983" "hsa01100"
> kegg[[2]][1]
[1] "hsa00232"
> tmp1<-substr(kegg[[2]][1],4,8) 番号だけを抽出
> tmp1
[1] "00232"
> mypath1<-unlist(mget(tmp1,KEGGPATHID2NAME,ifnotfound=list(NA)))
＝＞KEGG PathwayIDからKEGG Pathway Nameにマップするオブジェクト
> mypath1
00232
"Caffeine metabolism"
--------------------------------
> biocLite("KEGGREST")
BioC_mirror: https://bioconductor.riken.jp
U
downloaded 148 KB
Old packages: 'manipulate', 'class', 'foreign', 'MASS', 'nlme', 'nnet',
'spatial'
Update all/some/none? [a/s/n]:
n
> library(KEGGREST)
> genes<-keggGet("hsa:1045")
> genes
[[1]]
[[1]]$ENTRY
CDS
"1045"
[[1]]$NAME
[1] "CDX2, CDX-3, CDX2/AS, CDX3"
[[1]]$DEFINITION
[1] "(RefSeq) caudal type homeobox 2"
[[1]]$ORTHOLOGY
K09312
"homeobox protein CDX"
[[1]]$ORGANISM
hsa
"Homo sapiens (human)"
[[1]]$BRITE
[1] "Transcription factors [BR:hsa03000]" " Eukaryotic Type"
[3] " Helix-turn-helix" " Homeo domain only, Cad"
[5] " 1045 (CDX2)"
[[1]]$POSITION
[1] "13q12.3"
[[1]]$MOTIF
[1] "Pfam: Caudal_act Homeobox Homeobox_KN"
[[1]]$DBLINKS
[1] "NCBI-ProteinID: NP_001256" "NCBI-GeneID: 1045"
[3] "OMIM: 600297" "HGNC: 1806"
[5] "HPRD: 02622" "UniProt: Q99626"
[[1]]$AASEQ
A AAStringSet instance of length 1
width seq
[1] 313 MYVSYLLDKDVSMYPSSVRHSGGLNLAPQNFVSP...EPLSPVSSLQASVSGSVPGVLGPTGGVLNPTVTQ
[[1]]$NTSEQ
A DNAStringSet instance of length 1
width seq
[1] 942 ATGTACGTGAGCTACCTCCTGGACAAGGACGTGA...TGGGGGGGTGCTAAACCCCACCGTCACCCAGTGA