[BioC] Calculate coverage on genome.

[Fabrice Tourre]

Dear Martin,
I am appreciated for you suggestion.
I found in GenomicFeatures, there are such method:
transcriptsBy, exonsBy, cdsBy, intronsByTranscript,
fiveUTRsByTranscript, threeUTRsByTranscript.

So maybe I can used these method to got the coverage on exons, cds,
transcripts, introns, 3'utr and 5'utr. Do you have some ideas how to
got the coverages on promoter regions? For example, up to TSS 5kb
regions.
Thanks.

On Tue, Mar 15, 2011 at 9:17 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 03/15/2011 12:19 PM, Fabrice Tourre wrote:
>>
>> What's more, how many covaged the repeat region and unique region?
>
> Hi Fabrice --
>
> The steps in the work flow might invovle: input reads
>
>  library(GenomicRanges)
>  aln <- readGappedAlignemnts(<...>))
>
> and create regions of interest, e.g., from
>
>  library(GenomicFeatures)
>  txdb <- makeTranscriptDbFromUCSC(<...>)
>  cds <- cdsBy(txdb, "gene")
>
> or using the biomaRt or AnnotationDbi packages. Then count reads in each
> region of interest
>
>  hits <- countOverlaps(aln, cds)
>
> or calculate coverage and take views based on your regions of interest
>
>  cvg <- coverage(aln)
>  v <- Views(cvg, ranges(cds))
>
> and then summarize, e.g., viewSums. Maybe others will contribute more
> detail.
>
> Martin
>
>>
>> On Tue, Mar 15, 2011 at 8:18 PM, Fabrice Tourre<fabrice.ciup at gmail.com>
>>  wrote:
>>>
>>> Dear list,
>>> I am analysis mouse MeDIP-seq data, I want to know what percent reads
>>> coveraged the promter, 3'UTR, 5'UTR, intron and Exon region. Is there
>>> any packages can do this?
>>> Thank you very much in advance.
>>>
>>
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>
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