[BioC] Calculate coverage on genome.

[Martin Morgan]

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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