geneID转换之org.Hs.eg.db包简介

1）安装载入

if("org.Hs.eg.db" %in% rownames(installed.packages()) == FALSE) {source("http://bioconductor.org/biocLite.R");biocLite("org.Hs.eg.db")}
suppressMessages(library(org.Hs.eg.db))

2)查看该包所有的对象

ls("package:org.Hs.eg.db")

功能：

org.Hs.egACCNUM：Map Entrez Gene identi?ers to GenBank Accession Numbers
org.Hs.egALIAS2EG：Map between Common Gene Symbol Identi?ers and Entrez Gene
org.Hs.eg.db：Bioconductor annotation data package
org.Hs.egCHR：Map Entrez Gene IDs to Chromosomes
org.Hs.egCHRLENGTHS：A named vector for the length of each of the chromosomes
org.Hs.egCHRLOC：Entrez Gene IDs to Chromosomal Location
org.Hs.egENSEMBL：Map Ensembl gene accession numbers with Entrez Gene identi?ers
org.Hs.egENSEMBLPROT：Map Ensembl protein acession numbers with Entrez Gene identi?ers
org.Hs.egENSEMBLTRANS：Map Ensembl transcript acession numbers with Entrez Gene identi?ers
org.Hs.egENZYME：Map between Entrez Gene IDs and Enzyme Commission (EC) Numbers
org.Hs.egGENENAME：Map between Entrez Gene IDs and Genes
org.Hs.egGO：Maps between Entrez Gene IDs and Gene Ontology (GO) IDs
org.Hs.egMAP：Map between Entrez Gene Identi?ers and cytogenetic：Maps/bands
org.Hs.egMAPCOUNTS Number of：Mapped keys for the：Maps in package org.Hs.eg.db
org.Hs.egOMIM：Map between Entrez Gene Identi?ers and Mendelian Inheritance in Man (MIM) identi?ers
org.Hs.egORGANISM：The Organism for org.Hs.eg
org.Hs.egPATH：Mappings between Entrez Gene identi?ers and KEGG pathway identi?ers
org.Hs.egPFAM：Maps between Manufacturer Identi?ers and PFAM Identi?ers
org.Hs.egPMID：Map between Entrez Gene Identi?ers and PubMed Identi?ers
org.Hs.egPROSITE：Maps between Manufacturer Identi?ers and PROSITE Identi?ers
org.Hs.egREFSEQ：Map between Entrez Gene Identi?ers and RefSeq Identi?ers
org.Hs.egSYMBOL：Map between Entrez Gene Identi?ers and Gene Symbols
org.Hs.egUNIGENE：Map between Entrez Gene Identi?ers and UniGene cluster identi?ers
org.Hs.egUNIPROT：Map Uniprot accession numbers with Entrez Gene identi?ers
org.Hs.eg_dbconn：Collect information about the package annotation DB

3）各个对象的简单使用

3.1）org.Hs.egACCNUM

该作用是将 Entrez Gene identi?ers( https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) 与 GenBank accession numbers进行简单的mapping。依据的数据库是Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA

以其中一个gene2ensembl为例：

wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz

其中第一列是物种id，第二列是GeneID, 第三列是Ensemble_geneID,第四列是RNA_id,第五列是Ensemble_RNAid,第六列是protein_id

x <- org.Hs.egACCNUM  ### Bimap interface
mapped_genes <- mappedkeys(x) ## Get the entrez gene identifiers that are mapped to an ACCNUM
xx <- as.list(x[mapped_genes]) # Convert to a list
if(length(xx) > 0) {
xx[1:5]     # Get the ACCNUM for the first five genes
xx[[1]]     # Get the first one
}
#For the reverse map ACCNUM2EG:
xx <- as.list(org.Hs.egACCNUM2EG)  # Convert to a list
if(length(xx) > 0){
xx[1:5]      # Gets the entrez gene identifiers for the first five Entrez Gene IDs
xx[[1]]      # Get the first one
}