biomarRT conversion of symbols

Question

I wanted to use the code to convert mouse to human symbol, but I have problem with the mirror, I've tried to establish another one, but continue to have the same problem.

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)

}

score 1 · Answer 1 · edited Nov 16 '23 at 20:29

My background in coding is more extensive in Python. If you have Python skills, I can say for sure, use the Bioservices library:

from bioservices import BioMart

Install Bioservices via pip:

pip install bioservices

You can also use the web-based tool on Ensembl called BioMart. It does the same thing, just easier to use if you continue to have difficulties with Python or in your case, R. I looked up the R package for BioMart, it is called: biomaRt

Here's the link for the Ensembl BioMart web-based tool if you need to use it and are in a crunch for time on your project:

https://useast.ensembl.org/info/data/biomart/how_to_use_biomart.html#introduction

I hope this helps! :)

biomarRT conversion of symbols

Basic function to convert mouse to human gene names

1 Answers1