Biological Id转换（富集分析时）

第一种方法

mapIds(x, keys, column, keytype, …, multiVals)
参数：
x——the AnnotationDb object
keys——the keys to select records for from the database
column——the column to search on (for mapIds)
keytype——the keytype that matches the keys used

library(AnnotationDbi)
gene<-c('CCDC136','LINC00917','DBT','MDM4','JAKMIP1')
t1<-mapIds(org.Hs.eg.db, gene, 'ENTREZID', 'SYMBOL')

# CCDC136 LINC00917       DBT      MDM4   JAKMIP1
# "64753"  "732275"    "1629"    "4194"  "152789"

第二种方法

bitr(geneID, fromType, toType, OrgDb, drop = TRUE)
参数：
geneID——input gene id
fromType——input id type
toType——output id type
OrgDb——annotation db
drop——drop NA or not

t2<- bitr(gene, fromType = "SYMBOL",toType = 'ENTREZID',OrgDb = org.Hs.eg.db)

#      SYMBOL ENTREZID
# 1   CCDC136    64753
# 2 LINC00917   732275
# 3       DBT     1629
# 4      MDM4     4194
# 5   JAKMIP1   152789

fromType和toType取决于OrgDb。 idTypes <- idType(OrgDb)
对于org.Hs.eg.db而言，idType(org.Hs.eg.db)

# [1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT"  
"ENSEMBLTRANS"
# [6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL"  
"GENENAME"
# [11] "GO" "GOALL" "IPI"  "MAP" "OMIM"
# [16] "ONTOLOGY"  "ONTOLOGYALL"  "PATH" "PFAM"  "PMID"
# [21] "PROSITE" "REFSEQ" "SYMBOL" "UCSCKG" "UNIGENE"
# [26] "UNIPROT"

第三种方法

bitr_kegg(geneID, fromType, toType, organism, drop = TRUE)
其中，fromType, toType:“Path”, “Module”, “ncbi-proteinid”, “ncbi-geneid”, “uniprot”, “kegg”

t3<- bitr_kegg(t2$ENTREZID, fromType='ncbi-geneid', toType="ncbi-proteinid",organism='hsa')

#  ncbi-geneid ncbi-proteinid
#1      152789   NP_001293062
#2        1629      NP_001909
#3        4194      NP_002384
#4       64753      NP_073579