This is a sensible request, as it would be consistent with the behavior for RangesList and RangedData. Anyone opposed to this change?
On Tue, Nov 30, 2010 at 6:43 AM, Anna Terry <[email protected]>wrote: > Hi, > > Would it be possible for the BSgenome function getSeq to return the + > strand by default when given a GRanges object where the strand is "*" rather > than throw an error? The strand is not known for ChIP-seq regions and so it > is sensible to have the strand as "*" when storing them in a GRanges object. > > Anna > > > problem.gr > GRanges with 1 range and 6 elementMetadata values > seqnames ranges strand | score count unique > <Rle> <IRanges> <Rle> | <numeric> <integer> <integer> > [1] chr5 [125821746, 125821945] * | 97.02651 124 116 > ref.count height max > <integer> <numeric> <numeric> > [1] 10 29.03108 125821846 > > seqlengths > chr1 chr2 chr3 ... chrY_random chrUn_random > 197195432 181748087 159599783 ... 58682461 5900358 > > > problem.seq <- getSeq(Mmusculus, problem.gr) > Error in .extractSeqsFromDNAString(subject, ranges(grg), strand(grg)) : > 'strand' elements must be "+" or "-" > Calls: getSeq ... lapply -> lapply -> FUN -> .extractSeqsFromDNAString > > > problem.seq <- getSeq(Mmusculus, problem.gr, strand="+") > Error in .extractSeqsFromDNAString(subject, ranges(grg), strand(grg)) : > 'strand' elements must be "+" or "-" > Calls: getSeq ... lapply -> lapply -> FUN -> .extractSeqsFromDNAString > > > problem.seq <- getSeq(Mmusculus, seqnames(problem.gr), start=start( > problem.gr), end=end(problem.gr)) > # works > > > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB > [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB > [7] LC_PAPER=en_GB LC_NAME=en_GB LC_ADDRESS=en_GB > [10] LC_TELEPHONE=en_GB LC_MEASUREMENT=en_GB > LC_IDENTIFICATION=en_GB > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] XML_3.2-0 BSgenome.Mmusculus.UCSC.mm9_1.3.16 > [3] BSgenome_1.16.5 GenomicRanges_1.0.9 > [5] Biostrings_2.16.9 IRanges_1.6.17 > [7] rkward_0.5.3 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 tools_2.11.1 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
