You could call coverage on all sorts of things. How are you representing your reads? GappedAlignments would work, for example.
> showMethods(coverage) Function: coverage (package IRanges) x="AlignedXStringSet0" x="GRangesList" x="GappedAlignments" x="GenomicRanges" x="IRanges" x="MIndex" x="MaskCollection" x="MaskedXString" x="PairwiseAlignedFixedSubject" x="PairwiseAlignedFixedSubjectSummary" x="RangedData" x="RangesList" x="Views" x="numeric" On Fri, Jul 22, 2011 at 3:24 PM, Kunbin Qu <k...@genomichealth.com> wrote: > Steve, thanks for the advice. But I did not get it: coverage() is applied > to a set of IRanges. What should I use for the input of the coverage() then? > Is it possible for you to show me a little pseudo or real code? Thanks.*** > * > > ** ** > > -Kunbin**** > > ** ** > > ** ** > > *From:* Michael Lawrence [mailto:lawrence.mich...@gene.com] > *Sent:* Friday, July 22, 2011 3:15 PM > *To:* Kunbin Qu > *Cc:* bioc-sig-sequencing@r-project.org > *Subject:* Re: [Bioc-sig-seq] count the coverage base by base**** > > ** ** > > coverage(), form Views() on the coverage for your genes and then > viewSums().**** > > On Fri, Jul 22, 2011 at 2:36 PM, Kunbin Qu <k...@genomichealth.com> wrote:* > *** > > Hi, > > If I want to count the coverage base by base, not read by read, can I still > use countOverlaps? I have a human transcriptome done, and would like to > count the coverage for each gene based on the mapping. As there are some > reads mapped across the junctions (ie, one read is splitted into two > portions), or partially mapped into the introns, it would be good to count > the coverage by base pair, instead of by read number? Could anybody suggest > a way doing that? Thanks. > > -Kunbin > > > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to postmas...@genomichealth.com and delete this message, along with > any attachments, from your computer. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing**** > > ** ** > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to postmas...@genomichealth.com and delete this message, along with > any attachments, from your computer. > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
