GetBM gives controversial results

Question

[lizaveta]

I want to get chromosome location of SMARCA1 gene.

library("biomaRt")
human = useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl",host="grch37.ensembl.org", path="/biomart/martservice")
getBM(attributes = c("hgnc_symbol","chromosome_name", "start_position", 
                     "end_position","strand"),
     filters = "hgnc_symbol", values = "SMARCA1", mart = human)

I have a table after running this code:

hgnc_symbol chromosome_name start_position end_position strand
1     SMARCA1               X      128580480    128657477     -1

Then, I search for this very gene in the region it should be located:

getBM(attributes = c("hgnc_symbol","chromosome_name", "start_position", "end_position","strand", "transcript_length","ensembl_transcript_id"),
filters = c("chromosome_name","start","end"),
values = list("chrX", 128580480, 128657477),mart = human)

and get nothing:

[1] hgnc_symbol           chromosome_name       start_position        end_position          strand                transcript_length     ensembl_transcript_id
<0 rows> (or 0-length row.names)

How is this possible?

[Kevin Blighe]

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Answer 1

[russhh]

set chromosome_name to X not chrX in your getBM