Hi Ramzi,
Ramzi TEMANNI 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 ?
Yes. You are giving the start position, but not the end. Without
explicitly telling the Biomart server where to stop looking for genes,
where do you think it will stop by default?
Also, several of your coordinates are nonsensical. For instance, chr12
is only 133851859 bases long, chr20 is 63025520 bases long, etc.
Best,
Jim
Thanks in advance for your help
Best Regards,
Ramzi
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University of Michigan
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