gene.mapping {Pigengene} | R Documentation |
Takse as input gene IDs in a convention, say REFSEQ, and converts them to another convention.
gene.mapping(ids, inputType = "REFSEQ", outputType = "SYMBOL", leaveNA = TRUE, inputDb = "Human", outputDb = inputDb, verbose = 0)
ids |
A character vector of input gene IDs |
inputType |
The type of input IDs. |
outputType |
The type of output IDs. If it is a character vector, mapping will be done for each element. |
leaveNA |
If |
inputDb |
The input data base. Use |
outputDb |
The output data base. If it is a list, mapping will be done for each element. |
verbose |
The integer level of verbosity. 0 means silent and higher values produce more details of computation. |
It can map homologous genes between species e.g. from mouse to human. If more than 1 ID found for an input gene, only one of them is returned.
A matrix of characters with 3 columns: input, output1, and
output2. The last one is guaranteed not to be NA
.
Amir Foroushani, Habil Zare, and Rupesh Agrahari
Pages H, Carlson M, Falcon S and Li N. AnnotationDbi: Annotation Database Interface. R package version 1.32.3.
AnnotationDb-class
,
org.Hs.eg.db
org.Mm.eg.db
library(org.Hs.eg.db) g1 <- gene.mapping(ids="NM_001159995") print(g1) ## Mapping to multiple convention library(org.Mm.eg.db) g2 <- gene.mapping(ids=c("NM_170730", "NM_001013580"), inputType="REFSEQ", inputDb=org.Mm.eg.db, outputType=c("SYMBOL","ENTREZID"), outputDb=list(org.Hs.eg.db,org.Mm.eg.db), verbose=1) print(g2)