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 ?
Thanks in advance for your help
Best Regards,
Ramzi
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