[BioC] Gene-snp matching

[Mohamed Lajnef]

Dear James & Bucher

Thank you  very much for your help

Mohamed


James W. MacDonald a écrit :
> 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
>>
>


-- 
Mohamed Lajnef
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