[Bioc-devel] [BioC] readGappedAlignments and param argument

Elena Grassi grassi.e at gmail.com
Tue Sep 10 12:40:50 CEST 2013

> 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 :)

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