> You can use summarizeOverlaps with a 'BamFileList' created by something like
>
> myFiles = dir("/some/dir", pattern="bam$")
> bfl = BamFileList(myFiles, yieldSize=1000000)
> olaps = summarizeOverlaps(features, bfl)
>
> see the example on the help page
>
> method?"summarizeOverlaps,GRanges,BamFileList"
I see, thanks. Right now I was looking for a solution "prior" to
summarizeOverlaps due to the structure that I've given to my package -
but I will re-think about it and
check if in this way it works (I only have 20 unittest or so to
rewrite, no worries for me :) ).
Right now I've found a way to define the single chromosome GRanges
that works with "which=..." and I would like to offer flexibility
for people with small RAM...therefore running the whole analysis on
one chr at a time seems a reasonable option all the same.
>> http://comments.gmane.org/gmane.comp.lang.r.sequencing/755
>
>
> one small thing that came out of that thread was that
>
> as(seqinfo(BamFile("/some/file")), "GRanges")
>
> gives a GRanges of all the sequence lengths.
I saw that but I wanted to avoid having to do that for every bam and
merge the results afterwards - working at the "annotation" level
seemed more sensible to me.
I guess that I should have asked my boss to have 1 month to scavenge
around mans and vignettes before starting to write my first
bioconductor-R package :)
E.
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