Question: GetBM gives controversial results
0
gravatar for lizaveta
11 months ago by
lizaveta0
lizaveta0 wrote:

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?

biomart bioconductor R gene • 397 views
ADD COMMENTlink written 11 months ago by lizaveta0

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 11 months ago by Kevin Blighe46k
7
gravatar for russhh
11 months ago by
russhh4.6k
UK, U. Glasgow
russhh4.6k wrote:

set chromosome_name to X not chrX in your getBM

ADD COMMENTlink written 11 months ago by russhh4.6k
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