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 <KQu@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.michael@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 <KQu@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
>
>
>
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