[BioC] Indexing an RleList by GRanges

Johnston, Jeffrey jjj at stowers.org
Tue Apr 15 15:44:29 CEST 2014


Hello,

I really like this new ability to index into an RleList via a GRanges:

rl <- RleList(chr1=1:100)
gr <- GRanges(ranges=IRanges(10, 20), strand="+", seqnames="chr1")
rl[gr]

# RleList of length 1
# $chr1
# integer-Rle of length 11 with 11 runs
#   Lengths:  1  1  1  1  1  1  1  1  1  1  1
#   Values : 10 11 12 13 14 15 16 17 18 19 20

Would it be possible to make it strand-aware so that the values are reversed for ranges on the negative strand? Currently, the strand of each range appears to have no effect:

strand(gr) <- “-“
rl[gr]

# RleList of length 1
# $chr1
# integer-Rle of length 11 with 11 runs
#   Lengths:  1  1  1  1  1  1  1  1  1  1  1
#   Values : 10 11 12 13 14 15 16 17 18 19 20

This would make it more consistent with things like getSeq(), which are aware of negative-stranded GRanges.

Thanks!
Jeff


> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicRanges_1.16.0 GenomeInfoDb_1.0.1   IRanges_1.22.2       BiocGenerics_0.10.0  setwidth_1.0-3     

loaded via a namespace (and not attached):
[1] XVector_0.4.0 stats4_3.1.0 


More information about the Bioconductor mailing list