problem about using 'rtracklayer' to retrieve chromosome position of SNPs
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li lilingdu ▴ 450
@li-lilingdu-1884
Last seen 6.6 years ago
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? thanks! LiGang
rtracklayer rtracklayer • 1.0k views
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