[BioC] selecting score(GRanges_object) based on coordinates

[Philip Lijnzaad]

   Hi Michael,
   thanks for the elaborate anwer.

   Note that this solution assumes that the data are on one chromosome.

   hmm,  it seems to work with the coverage being for all chromomes; I iterate
   over the features (each of them contiguous and on one chromosome only).

   You want:
   scores <- coverage(coverage, weight="score")

   OK, but the coverage was read from a bigwig file, so in this case it would
   not work I think.

   scores[as(feature, "RangesList")]
   Make sure that the seqlevels are the same between "coverage" and "feature".

   OK, good point.

   However, in this case fastest way is to have rtracklayer load the coverage
   directly as an Rle. In release, this is just
   scores <- import("[1]my.bw", asRle=TRUE)
   scores[ as(feature, "RangesList") ]

   I was actually  been looking for something that, but this is not available
   my version (R 3.0.1, Bioconductor 2.12, rtracklayer 1.20.4)

   If you are *only* interested in the data over "feature", then you could tell
   rtracklayer to only load that data (the rest of the RleList will be zeroed
   out).

   scores <- import("[2]my.bw", asRle=TRUE, which=feature)
   feature.scores <- scores[ as(feature, "RangesList") ]
   If "feature" is contained within one chromosome, then you might want to
   simply:
   unlist(feature.scores, use.names=FALSE)

   OK

   With all that explained, it would be nice to know your use case. Often these
   types of problems are solvable with RleViews[List].

   Well, I was interested in the behaviour of protein-DNA binding data (for
   which I have external bigwig files) over the promoters of a certain set of
   genes. I would have hoped there to be a clear-cut example on the interwebs.
   I guess there is one now (i.e. this thread :-), but still it would be nice
   to be in one of the vignettes.
   Thanks again,
   Philip
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References

   1. http://my.bw/
   2. http://my.bw/