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 Numbersorg.Hs.egALIAS2EG：Map between Common Gene Symbol Identi?ers and Entrez Geneorg.Hs.eg.db：Bioconductor annotation data packageorg.Hs.egCHR：Map Entrez Gene IDs to Chromosomesorg.Hs.egCHRLENGTHS：A named vector for the length of each of the chromosomesorg.Hs.egCHRLOC：Entrez Gene IDs to Chromosomal Locationorg.Hs.egENSEMBL：Map Ensembl gene accession numbers with Entrez Gene identi?ersorg.Hs.egENSEMBLPROT：Map Ensembl protein acession numbers with Entrez Gene identi?ersorg.Hs.egENSEMBLTRANS：Map Ensembl transcript acession numbers with Entrez Gene identi?ersorg.Hs.egENZYME：Map between Entrez Gene IDs and Enzyme Commission (EC) Numbersorg.Hs.egGENENAME：Map between Entrez Gene IDs and Genesorg.Hs.egGO：Maps between Entrez Gene IDs and Gene Ontology (GO) IDsorg.Hs.egMAP：Map between Entrez Gene Identi?ers and cytogenetic：Maps/bandsorg.Hs.egMAPCOUNTS Number of：Mapped keys for the：Maps in package org.Hs.eg.dborg.Hs.egOMIM：Map between Entrez Gene Identi?ers and Mendelian Inheritance in Man (MIM) identi?ersorg.Hs.egORGANISM：The Organism for org.Hs.egorg.Hs.egPATH：Mappings between Entrez Gene identi?ers and KEGG pathway identi?ersorg.Hs.egPFAM：Maps between Manufacturer Identi?ers and PFAM Identi?ersorg.Hs.egPMID：Map between Entrez Gene Identi?ers and PubMed Identi?ersorg.Hs.egPROSITE：Maps between Manufacturer Identi?ers and PROSITE Identi?ersorg.Hs.egREFSEQ：Map between Entrez Gene Identi?ers and RefSeq Identi?ersorg.Hs.egSYMBOL：Map between Entrez Gene Identi?ers and Gene Symbolsorg.Hs.egUNIGENE：Map between Entrez Gene Identi?ers and UniGene cluster identi?ersorg.Hs.egUNIPROT：Map Uniprot accession numbers with Entrez Gene identi?ersorg.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 interfacemapped_genes <- mappedkeys(x) ## Get the entrez gene identifiers that are mapped to an ACCNUMxx <- as.list(x[mapped_genes]) # Convert to a listif(length(xx) > 0) {xx[1:5]     # Get the ACCNUM for the first five genesxx[[1]]     # Get the first one}#For the reverse map ACCNUM2EG:xx <- as.list(org.Hs.egACCNUM2EG)  # Convert to a listif(length(xx) > 0){xx[1:5]      # Gets the entrez gene identifiers for the first five Entrez Gene IDsxx[[1]]      # Get the first one}

原文地址：https://www.cnblogs.com/djx571/p/9612719.html