[Bioc-devel] "score" column disappeared when importing bigWigs w/ rtracklayer:::import.bw in R-devel?

[Steve Lianoglou]

Hi,

I've been chasing my tail for a while on this -- I'm trying to import
some data from a bigWig files using R-2.14 and R-devel.

Seems like mostly-current R-devel + bioc packages isn't happy for some reason.

Consider this snipped using R-2.14 on a BigWigFile object of interest:

R> import.bw(bwf, BigWigSelection(GRanges("chrX_random",
IRanges(104857,104931))))
RangedData with 75 rows and 1 value column across 1 space
          space           ranges   |     score
       <factor>        <IRanges>   | <numeric>
1   chrX_random [104857, 104857]   |    -0.424
2   chrX_random [104858, 104858]   |     0.971
3   chrX_random [104859, 104859]   |     1.381
4   chrX_random [104860, 104860]   |     2.146
5   chrX_random [104861, 104861]   |     4.665
6   chrX_random [104862, 104862]   |     3.966
7   chrX_random [104863, 104863]   |     1.012
8   chrX_random [104864, 104864]   |     4.161
9   chrX_random [104865, 104865]   |     2.412
...         ...              ... ...       ...

Same file, same selection using R-devel

R> import.bw(bwf, BigWigSelection(GRanges("chrX_random",
IRanges(104857,104931))))
RangedData with 75 rows and 0 value columns across 1 space
          space           ranges   |
       <factor>        <IRanges>   |
1   chrX_random [104857, 104857]   |
2   chrX_random [104858, 104858]   |
3   chrX_random [104859, 104859]   |
4   chrX_random [104860, 104860]   |
5   chrX_random [104861, 104861]   |
6   chrX_random [104862, 104862]   |
7   chrX_random [104863, 104863]   |
8   chrX_random [104864, 104864]   |
9   chrX_random [104865, 104865]   |
...         ...              ... ...

Strangely a call to `summary` works in R-devel and gives the same
result as it does in R-2.14:

R> summary(bwf, GRanges("chrX_random", IRanges(104857,104931)))
SimpleRleList of length 1
[[1]]
'numeric' Rle of length 1 with 1 run
  Lengths:                1
  Values : 2.46041230119978


This is my sesionInfo for R-devel:

R Under development (unstable) (2011-11-04 r57571)
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] rtracklayer_1.15.7   GenomicRanges_1.7.26 IRanges_1.13.24
[4] BiocGenerics_0.1.4

loaded via a namespace (and not attached):
[1] Biostrings_2.23.6 bitops_1.0-4.1    BSgenome_1.23.2   RCurl_1.91-1
[5] Rsamtools_1.7.35  tools_2.15.0      XML_3.6-2         zlibbioc_1.1.0


-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact