Hi Mohamed,
First, you don't need to ask the same question twice with different
subject lines; the list traffic is typically low over the weekend, so
you could have waited until today for a response. In addition, you
will
either get a response or not - asking again probably reduces your
chances of getting an answer.
Mohamed Lajnef wrote:
> Hi All,
>
> I have a list of genes and I want the snps matching of these genes
(the
> other way too e.g: Snps ----> genes)
>
> Is there any R package to do this ?
Several. You can do this with either an org.Xx.eg.db package in
concert
with a SNPloc package, using biomaRt, or RMySQL with a direct query of
the UCSC genome browser public MySQL server.
1.)
library(org.Hs.eg.db)
library("SNPlocs.Hsapiens.dbSNP.20080617")
gns <- c("VEGFA","TP53", "BRCA1")
egs <- unlist(mget(gns, org.Hs.egALIAS2EG))
beg <- mget(egs, org.Hs.egCHRLOC)
finish <- mget(egs, org.Hs.egCHRLOCEND)
chr6 <- getSNPlocs("chr6")
chr6[chr6$loc > beg[[1]] & chr6$loc < finish[[1]],]
RefSNP_id alleles_as_ambig loc
215667 2010963 S 43846328
215668 6928818 R 43846352
215669 25648 Y 43846955
215670 58159269 Y 43847424
215671 61085192 R 43847452
<snip>
2.)
mart <- useMart("snp","hsapiens_snp")
embl <- unlist(mget(egs, org.Hs.egENSEMBL))
snps <- getBM(c("ensembl_gene_stable_id", "refsnp_id"),"ensembl_gene",
embl , mart)
head(snps)
ensembl_gene_stable_id refsnp_id
1 ENSG00000012048 rs2355954
2 ENSG00000012048 rs35578914
3 ENSG00000012048 rs3074670
4 ENSG00000012048 rs34130132
5 ENSG00000012048 rs762533
6 ENSG00000012048 rs762532
<snip>
3.)
library(RMySQL)
con <- dbConnect("MySQL", user = "genome", host =
"genome-mysql.cse.ucsc.edu", dbname = "hg18")
sql <- paste("select name from snp128 where chrom='chr6' and
chromStart
between", beg[[1]], "and", finish[[1]], ";")
dbGetQuery(con, sql)
dbGetQuery(con, sql)
name
1 rs2010963
2 rs6928818
3 rs25648
4 rs35440538
5 rs833067
6 rs1885657
7 rs943070
8 rs1413711
<snip>
I leave it as an exercise to figure out how to go the other direction.
Best,
Jim
>
> Regards
> M
>
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
