Human to mouse gene (R, biomaRt)

Converting Human to mouse genes names with BiomaRt

human -> mouse

#install
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("biomaRt")


#human -> mouse
require("biomaRt") 

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")

x <- c("HMMR", "TLX3","CPEB4") #humGenes

genesV2 <- getLDS(attributes = c("hgnc_symbol"),
                  filters = "hgnc_symbol",
                  values = x,
                  mart = human, 
                  attributesL = c("mgi_symbol"), 
                  martL = mouse,
                  uniqueRows=T)
genesV2

#참고
Human gene symbol = hgnc_symbol /Human = Homo sapiens = Hsapiens
Mouse gene symbol = mgi_symbol / Mouse = Mus musculus = Mmusculus

결과

> genesV2
  HGNC.symbol MGI.symbol
1       CPEB4      Cpeb4
2        HMMR       Hmmr
3        TLX3       Tlx3

Mouse -> Human 으로 하고싶다면 반대로 하면 된다.


#getLDS
:Retrieves information from two linked datasets

=This function is the main biomaRt query function that links 2 datasets and retrieves information from these linked BioMart datasets. In Ensembl this translates to homology mapping.
reference: https://rdrr.io/bioc/biomaRt/man/getLDS.html

getLDS: Retrieves information from two linked datasets in biomaRt: Interface to BioMart databases (i.e. Ensembl)

reference: Converting mouse to human gene names with biomaRt package | R-bloggers

Bioconductor - biomaRt