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
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