[BioC] problem about using 'rtracklayer' package to retrieve SNP chromosome position

[James W. MacDonald]

Hi LiGang,

LiGang wrote:
> Dear list,
> 
> using rtracklayer, it's possible to retrieve data with functions 
> of 'ucscTableQuery' and 'getTable'.
> however, these functions could only retrieve data given a genomic range.
> For example, using following code could retrieve snps between 10000 to 20000 
> basepair on chromosome 2.
> 
> ####======================
> library(rtracklayer)
> browserSession("UCSC")->session
> ucscTableQuery(session, "snp129",GenomicRanges(10000,20000, 2))->todo
> tableName(todo)<-"snp129"
> getTable(todo)
> ####======================
> 
> my question is how to retrieve data using identifiers(names/accessions).
> for example, is it possible to retrieve chromosome position given the rs 
> number of several SNPs, such as 
> rs10003974
> rs10087355
> rs10075230
> ...
> 
> is there any function in 'rtracklayer' package can do this?

I don't know if you can do this with rtracklayer, but it isn't difficult 
to do it with RMySQL.

 > library(RMySQL)
Loading required package: DBI
 > con <- dbConnect("MySQL", user = "genome", host = 
"genome-mysql.cse.ucsc.edu", dbname = "hg18")
 > snps <- scan("clipboard", what = "c")
Read 3 items
 > snps
[1] "rs10003974" "rs10087355" "rs10075230"
 > sql <- paste("select name, chrom, chromEnd from snp129 where name in 
('", paste(snps, collapse = "','"), "');", sep = "")
 > dbGetQuery(con, sql)
         name chrom  chromEnd
1 rs10003974  chr4 154710828
2 rs10075230  chr5  44862908
3 rs10087355  chr8  41531957

Or you could use biomaRt

 > mart <- useMart("snp", "hsapiens_snp")
Checking attributes ... ok
Checking filters ... ok
 > getBM(c("refsnp_id","chr_name","chrom_start"), "refsnp", snps, mart)
    refsnp_id chr_name chrom_start
1 rs10003974        4   154491378
2 rs10075230        5    44827151
3 rs10087355        8    41412800

Best,

Jim


> 
> thanks!
> 
> LiGang
> 
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-- 
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