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")

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