Converting mouse to human gene names with biomaRt package

October 14, 2016
By

(This article was first published on Let's talk about science with R, and kindly contributed to R-bloggers)

Converting mouse gene names to the human equivalent and vice versa is not always as straightforward as it seems, so I wrote a function to simplify the task. The function takes advantage of the getLDS() function from the biomaRt to get the hgnc symbol equivalent from the mgi symbol. For example, let’s convert the following mouse gene symbols, Hmmr, Tlx3, and Cpeb4, to their human equivalent.

musGenes <- c("Hmmr", "Tlx3", "Cpeb4")

# Basic function to convert mouse to human gene names
convertMouseGeneList <- function(x){

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

genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = x , mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T)
humanx <- unique(genesV2[, 2])

# Print the first 6 genes found to the screen
print(head(humanx))
return(humanx)
}

We can just as easily write a function to go from human to mouse genes.

# Basic function to convert human to mouse gene names
convertHumanGeneList <- function(x){

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

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

humanx <- unique(genesV2[, 2])

# Print the first 6 genes found to the screen
print(head(humanx))
return(humanx)
}

genes <- convertMouseGeneList(humGenes)

If you have any other suggestions on how to convert mouse to human gene names in R, I would love to hear them just email me at [email protected]

 

 

To leave a comment for the author, please follow the link and comment on their blog: Let's talk about science with R.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers


Sponsors

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)