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参考http://bioconductor.org/help/workflows/annotation/annotation/
Object type example package name contents
OrgDb org.Hs.eg.dbgenebased information for Homo sapiens
TxDb TxDb.Hsapiens.UCSC.hg19.knownGene transcriptome ranges for Homo sapiens
OrganismDb Homo.sapiens composite information for Homosapiens
BSgenome BSgenome.Hsapiens.UCSC.hg19 genome sequence for Homo sapiens
常用注释包:
source("http://bioconductor.org/biocLite.R")biocLite("AnnotationHub")biocLite ("org.Hs.eg.db")biocLite("Homo.sapiens")biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")biocLite("BSgenome.Hsapiens.UCSC.hg19")biocLite("biomaRt")biocLite("TxDb.Athaliana.BioMart.plantsmart22")
AnnotationHub:基因注释的hub
help(package="name")library("AnnotationHub")ah <- AnnotationHub()例子: UCSC,HG19,HOMO sapiens
ahs <- query(ah, "UCSC")ahs <- subset(ahs, ahs$genome=='hg19')ahs <- subset(ahs, ahs$species=='Homo sapiens')OrDb object:寻找基因名及其注释的相关信息
library(org.Hs.eg.db)db <- org.Hs.eg.dbkeytypes(db) [1] "ACCNUM" "ALIAS" "ENSEMBL" [4] "ENSEMBLPROT" "ENSEMBLTRANS" "ENTREZID" [7] "ENZYME" "EVIDENCE" "EVIDENCEALL" [10] "GENENAME" "GO" "GOALL" [13] "IPI" "MAP" "OMIM" [16] "ONTOLOGY" "ONTOLOGYALL" "PATH" [19] "PFAM" "PMID" "PROSITE" [22] "REFSEQ" "SYMBOL" "UCSCKG" [25] "UNIGENE" "UNIPROT"head(keys(db,keytype="GENENAME"))select(db,keys=genes,keytype="SYMBOL",col=c("UCSCKG"))
TxDb Objects:主要用于操作转录本
library("TxDb.Hsapiens.UCSC.hg19.knownGene")tdb <- TxDb.Hsapiens.UCSC.hg19.knownGenetdb 提取转录本等信息:txs <- transcripts(txdb)exons(txdb)cds(txdb)genes(txdb)promoters(txdb) 根据基因提取转录本信息:txby <- transcriptsBy(txdb, by="gene")txby BSgenome Objects :提取序列信息library("BSgenome")head(available.genomes())library("BSgenome.Hsapiens.UCSC.hg19")Archiver|手机版|科学网 ( 京ICP备07017567号-12 )
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