[Bioc-sig-seq] import.bw to Rle? [re-opened]

Cook, Malcolm MEC at stowers.org
Tue Aug 30 22:36:26 CEST 2011

Janet, Michael, and fellow Bioconductors,

I am trying to follow the helpful suggestion Michael made to Janet, found here  https://stat.ethz.ch/pipermail/bioconductor/2011-August/040729.html

for obtaining a Rle encoding of the contents of a bigWig file.

But instead get an error: "  'weight' must be a non-empty list of integers"

As per the following session.

I would appreciate any advice/hints.


-Malcolm Cook
Computational Biology - Stowers Institute for Medical Research

> library(IRanges)
> library(rtracklayer)
> bw <- import(test.bw.file, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7)))
> coverage(bw,weight="score")
Error in .local(x, shift, width, weight, ...) : 
  'weight' must be a non-empty list of integers

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] C

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

other attached packages:
[1] IRanges_1.10.6     rtracklayer_1.13.3 RCurl_1.5-0        bitops_1.0-4.1    

loaded via a namespace (and not attached):
[1] BSgenome_1.20.0     Biostrings_2.20.3   GenomicRanges_1.4.8
[4] XML_3.4-0          

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