Retrieve initial query in getBM()

Question

[helia.ziaei]

Hello,

I am writing a piece of code to retrieve some data using biomaRt from a given region. I have several regions in a list. I wonder if there is any way to get the initial "chromosomal_region" in the attributes. In the other words, I wanted to know each result is associated with what query.

Here is my command:

results=getBM(
  attributes = c("hgnc_symbol","ensembl_gene_id", "chromosome_name", "start_position", "end_position","gene_biotype"),
  filters = c("chromosomal_region"),
  values = list(chromosomal_region=unlist(as.list(data$query))),
  mart = ensemble)

and I want to have the chromosomal region in the output results.

[lessismore]

If it's not present in the "attribute" list you cannot include it. But you can add it later with the function findOverlaps from IRanges Bioconductor package.

Answer 1

[loughrae]

I don’t think that’s possible, probably because the chromosomal region is custom and not stored in the database as one of the gene attributes. You’d need to get it to return your filters, which I don’t think it does.

I deal with this by left-joining my table of chromosomal regions to the results using bedtools:

bedtools intersect -loj -a regions.bed -b ensemblgenes.bed > joined.bed

You’ll need to first convert your regions and results to bed format and save them as tab-delimited files before running this on the command line. You could alternatively use IRanges as @lessismore suggested, I just find bedtools more intuitive.