Get gene names from rs SNP ids for mmusculus_gene_ensembl
I have mouse data with an old mapping from rs SNP IDs to base pair position and chromosome. I would like to query Ensembl to get the genes and then the gene annotations for the rs SNP IDs in my data. When I go to the Ensembl website (useast.ensembl.org/Mus_musculus/Info/Index) with GRCm39, I can enter the rs ID and get information on that SNP. I would like to do this in code because I have about 250 SNPs that I want to look at.
I found this old post, that does what I want for homo sapiens: Get gene names from rs SNP ids
This code still works for homo sapiens. However, when changing it to the mouse genome GRCm39 (mmusculus_gene_ensembl), there does not seem to be a single filter by which I could query the database using the rs IDs.
Here is my code:
ensembl <- useEnsembl(biomart = "genes", dataset = "mmusculus_gene_ensembl")
filters <- listFilters(ensembl)
attributes = listAttributes(ensembl)
for (f in filters[,1]) {
print(f)
searchFilterOptions(mart = ensembl, filter = f, pattern = "rs")
}
None of the filters shows any results for any rs query.
Does anyone understand what I am doing wrong?
• 51 views
Read more here: Source link