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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
