R中的Biomart将rssnp转换为基因名称

Question

I have the following code in R.

library(biomaRt)

snp_mart = useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp")
snp_attributes = c("refsnp_id", "chr_name", "chrom_start", 
"associated_gene", "ensembl_gene_stable_id", "minor_allele_freq")

getENSG <- function(rs, mart = snp_mart) {
results <- getBM(attributes = snp_attributes,
               filters    = "snp_filter", values = rs, mart = mart)
return(results)
}

getENSG("rs144864312")

    refsnp_id chr_name chrom_start associated_gene ensembl_gene_stable_id
1 rs144864312        8    20254959              NA        ENSG00000061337
    minor_allele_freq
1       0.000399361

I have no background in biology so please forgive me if this is an obvious question. I was told that rs144864312 should match to the gene name "LZTS1". The code above I largely got from off the internet. My question is where do I extract that gene name from? I get that the listAttributes(snp_mart) gives a list of all possible outputs but I don't see any that give me the above "gene name". Where do I extract this gene name from using biomart (and given the rs number)? Thank you in advance.

PS: I need to do this for something like 500 entries (not just 1). Hence why I created a simple function as above to extract the gene name.

Answer 1

First I think your question will draw more professional attention on https://www.biostars.org/

That said, to my knowledge, now you have the ensembl ID (ENSG00000061337), you are just one step away from getting the gene name. If you google "how to convert ensembl ID to gene name" you will find many approaches. Here I list a few options:

1. use: https://david.ncifcrf.gov/conversion.jsp
2. use biomart under ensemble: http://www.ensembl.org/biomart/martview/1cb4c119ae91cb34b2cd5280be0a1aac
3. download a table with both gene name and ensembl ID, and customize your query. You might want to download it from UCSC Genome Browser, and here are some instructions: https://www.biostars.org/p/92939/

Good luck