Hi Sean
Thanks for your reply,
As i have short reads of 50b, I've modified the code accordigly to your
suggestion:
gn.m1<-getBM(attributes= c("hgnc_symbol"),
filters=c("chromosome_name","start",*"end"*),
values=list(t.cpd[1:10,1],as.numeric(t.cpd[1:10,2]),*
as.numeric(t.cpd[1:10,2])+50*), mart=ensembl)
But still having more genes :
hgnc_symbol
1 UBE2G1
2 DUSP5P
3 HIST3H2BA
4 ZNF847P
5 ACTBP11
6 ZC3H11B
........
8488 PPP2R2C
8489 WFS1
8490 SNORD73A
8491 SNORA24
8492 SNORA26
Did I miss something ?
Thanks again
Regards,
Ramzi
----------------------------------------------------------------
On Mon, Dec 7, 2009 at 3:57 PM, Sean Davis <[email protected]> wrote:
> On Mon, Dec 7, 2009 at 9:52 AM, Ramzi TEMANNI <[email protected]>
> wrote:
> > Hi,
> > I want to extract the gene names knowing the chromosome and the position
> for
> > each genes:
> >> t.cpd[1:10,1:2]
> > CHR.M1 POS.M1
> > [1,] "12" "140059033"
> > [2,] "19" "164634640"
> > [3,] "10" "32347784"
> > [4,] "11" "30576841"
> > [5,] "2" "86479831"
> > [6,] "12" "237019866"
> > [7,] "4" "76487174"
> > [8,] "20" "136121868"
> > [9,] "2" "6255547"
> > [10,] "1" "67658137"
> >
> > i use the following commands:
> > library(biomaRt)
> > mart = useMart("ensembl")
> > ensembl = useDataset("hsapiens_gene_ensembl", mart = mart)
> > gn.m1<-getBM(attributes= c("hgnc_symbol"),
> > filters=c("chromosome_name","start"),
> > values=list(t.cpd[1:10,1],t.cpd[1:10,2]), mart=ensembl)
> >
> > I'm expecting having a list of 10 genes names, but instead i get 8652
> genes:
> > hgnc_symbol
> > 1 OR2M1P
> > 2 OR2L1P
> > 3 HSD17B7P1
> > 4 OR14L1P
> > 5 OR2W5
> > 6 VN1R5
> > ......
> > 8649 WFS1
> > 8650 SNORD73A
> > 8651 SNORA24
> > 8652 SNORA26
> >
> > Did I miss something ?
>
> Your query will pull out all genes that are in the chromosomal regions
> STARTING with your start position. In other words, you are getting
> all of the genes that are to the right of the start positions. You
> probably want to specify an end position as well as a start position
> for your query.
>
> Sean
>
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