Question

Converting single GRanges object as per chromosome GRangeList

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Prashantha Hebbar ▴ 260

@prashantha-hebbar-3526

Last seen 5.0 years ago

Dear Friends, My following geneRange object has all chromosomal information in one GRange object. library(VariantAnnotation) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb = TxDb.Hsapiens.UCSC.hg19.knownGene txg = transcriptsBy(txdb,by="gene") > geneRange <- sort(unlist(range(txg[as.character(myGenes$geneId)]))) > geneRange GRanges with 11 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> 4067 chr8 [ 56792386, 56925006] + 26579 chr11 [ 69061622, 69156450] + 595 chr11 [ 69455873, 69469242] + 2017 chr11 [ 70244612, 70282690] + 10413 chr11 [101981192, 102104154] + 330 chr11 [102188181, 102210135] + 329 chr11 [102217966, 102249401] + 9965 chr11 [ 69513006, 69519106] - 2249 chr11 [ 69587797, 69590171] - 2248 chr11 [ 69624736, 69634192] - 47 chr17 [ 40023179, 40075272] - --- I have to get SNP and genotype information for the same from 1000 genome. Below code does that. However, each time I have to create ftp url and connect to 1000 Genome resource. thats painstaking. i=0 for(chr in as.vector(seqnames(geneRange))){ baseUrl <- paste("ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/ analysis_results/integrated_call_sets/ALL.chr",chr,".integrated_phase1 _v3.20101123.snps_indels_svs.genotypes.vcf.gz",sep="") i=i+1 print(baseUrl) inGene <- snpsInGene(geneRange[i],baseUrl,geno="GT",info=NA) print(inGene) } If I have my geneRange information as per chromosome in GRangeList form, my script becomes more efficient. because, I can retrive genotypes from each chromosomes in one go. So, May I know a way to convert geneRange GRange object to GRangeList Object as per chromosome number? Thanking you in anticipation. Regards, Prashantha [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.0 years ago by Steve Lianoglou ★ 13k • written 11.0 years ago by Prashantha Hebbar ▴ 260

score 1 · Answer 1 · 2013-12-03

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 21 months ago

United States

Hi, On Tue, Dec 3, 2013 at 6:35 AM, Prashantha Hebbar <prashantha.hebbar at="" yahoo.com=""> wrote: [snip] > If I have my geneRange information as per chromosome in GRangeList form, my script becomes more efficient. because, I can retrive genotypes from each chromosomes in one go. > So, May I know a way to convert geneRange GRange object to GRangeList Object as per chromosome number? [/snip] To answer your direct question: you can split a GRanges object into a GRangesList by its chromosome name like so (assume that your GRanges object is named `gr`): R> grl <- split(gr, seqnames(gr)) HTH, -steve -- Steve Lianoglou Computational Biologist Genentech

ADD COMMENT • link 11.0 years ago Steve Lianoglou ★ 13k

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Thank you. It works perfectly fine. Regards, Prashantha On Tuesday, December 3, 2013 8:18 PM, Steve Lianoglou <lianoglou.steve@gene.com> wrote: Hi, On Tue, Dec 3, 2013 at 6:35 AM, Prashantha Hebbar <prashantha.hebbar@yahoo.com> wrote: [snip] > If I have my geneRange information as per chromosome in GRangeList form, my script becomes more efficient. because, I can retrive genotypes from each chromosomes in one go. > So, May I know a way to convert geneRange GRange object to GRangeList Object as per chromosome number? [/snip] To answer your direct question: you can split a GRanges object into a GRangesList by its chromosome name like so (assume that your GRanges object is named `gr`): R> grl <- split(gr, seqnames(gr)) HTH, -steve -- Steve Lianoglou Computational Biologist Genentech [[alternative HTML version deleted]]

ADD REPLY • link 11.0 years ago Prashantha Hebbar ▴ 260