[BioC] Calculate coverage on genome.

[Martin Morgan]

On 03/16/2011 01:46 AM, Fabrice Tourre wrote:
> 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.

Hi Fabrice -- if you have the TSS (e.g., from 
start(transcriptsBy(<...))), you can easily create GRanges representing 
them, either directly using ?GRanges or ?GRangesList, or by manipulating 
an existing GRanges / GRangesList object with commands like flank, 
narrow, etc., as documented on for instance the GRanes help page. Martin

> 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.
>>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>> --
>> Computational Biology
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>
>> Location: M1-B861
>> Telephone: 206 667-2793
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793