[Bioc-sig-seq] coverage() is misbehaving with (apparently sound) GRanges object

[Ivan Gregoretti]

Hi all,

coverage(), naughty boy!

I have two GRanges instances

# my 100 million tags
> class(B)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"

# a few ChIP-seq peaks
> class(P)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"

# Now I want to keep only the tags in-peak
> BP <- B[B %in% P,]

# Are you ok BP?
> class(BP)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"
# Good.

# Now, whilst coverage(B) and coverage(P) work, BP crashes
> coverage(BP)
Error in coverage.normargWidth(width, length(x)) :
  'x' has no element and 'width' is NULL


BP is, I understand, I subset of B. Why would it crash coverage()?


Thank you,

Ivan

> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-03-25 r51410)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

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

other attached packages:
 [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 chipseq_0.3.5
 [3] ShortRead_1.5.21                   lattice_0.18-3
 [5] BSgenome_1.15.19                   Biostrings_2.15.25
 [7] GenomicRanges_0.0.9                IRanges_1.5.70
 [9] rtracklayer_1.7.11                 RCurl_1.3-1
[11] bitops_1.0-4.1

loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.12.0   hwriter_1.1   tools_2.12.0  XML_2.6-0