On 09/10/2013 03:40 AM, Elena Grassi wrote:
You can use summarizeOverlaps with a 'BamFileList' created by something like
myFiles = dir("/some/dir", pattern="bam$")
bfl = BamFileList(myFiles, yieldSize=100)
olaps = summarizeOverlaps(features, bfl)
see the example on the help page
> You can use summarizeOverlaps with a 'BamFileList' created by something like
>
> myFiles = dir("/some/dir", pattern="bam$")
> bfl = BamFileList(myFiles, yieldSize=100)
> olaps = summarizeOverlaps(features, bfl)
>
> see the example on the help page
>
> method?"summarizeOverlaps,GRanges
On 09/10/2013 12:22 AM, Elena Grassi wrote:
Ok, thanks - I misread the manual, I just thought that was a way to
filter out reads falling over certain regions.
After reading the alignments I use summarizeOverlaps to obtain counts
with the desired options. I decided to use scanBamParam(which=..)
Ok, thanks - I misread the manual, I just thought that was a way to
filter out reads falling over certain regions.
After reading the alignments I use summarizeOverlaps to obtain counts
with the desired options. I decided to use scanBamParam(which=..)
because loading bams and counting overlaps is us
