[BioC] A question about the function readGAlignmentPairs in GenomicRnages package

[Hervé Pagès]

On 03/30/2014 11:52 AM, Niu, Liang (NIH/NIEHS) [E] wrote:
> Sorry for the typo in the previous email. What I mean is "I do NEED (not NOT) the pairing information".

I see. So yes, readGAlignmentsList() should do it.

Cheers,
H.

>
> Liang
> ________________________________________
> From: Hervé Pagès [hpages at fhcrc.org]
> Sent: Sunday, March 30, 2014 2:51 PM
> To: Niu, Liang (NIH/NIEHS) [E]; bioconductor at r-project.org
> Subject: Re: A question about the function readGAlignmentPairs in GenomicRnages package
>
> On 03/30/2014 11:31 AM, Niu, Liang (NIH/NIEHS) [E] wrote:
>> Dear Herve,
>>
>> Thanks for your suggestion. I do not the paring information in the downstream analysis, therefore, readGAlignmentsList() is good.
>
> Maybe I was not clear enough but if you don't need the pairing, then
> you can just use readGAlignments(). readGAlignmentsList() will pair
> everything that can be paired and this has a cost (in terms of
> performance and memory usage). By using readGAlignments() you avoid
> that cost and you also end up with an object that is a little bit
> simpler to manipulate (i.e. a GAlignments instead of GAlignmentsList
> object).
>
> Hope that makes sense,
> H.
>
>>
>> Liang
>> ________________________________________
>> From: Hervé Pagès [hpages at fhcrc.org]
>> Sent: Sunday, March 30, 2014 2:12 PM
>> To: Niu, Liang (NIH/NIEHS) [E]
>> Cc: bioconductor at r-project.org
>> Subject: Re: A question about the function readGAlignmentPairs in GenomicRnages package
>>
>> Hi Liang,
>>
>> Hope you don't mind that I'm cc'ing the Bioconductor mailing list, so
>> other can give suggestions.
>>
>> On 03/30/2014 09:32 AM, Niu, Liang (NIH/NIEHS) [E] wrote:
>>> Dear Mr. Pages,
>>>
>>> This is Liang Niu, a research fellow at the National Institute of Environmental Health Sciences.
>>>
>>> I am using R to read .bam files for chromatin interaction data sets. Such data sets contains alignments for  paired-end reads from ChIA-PET experiment, thus it has pairs in which two reads on different chromosomes and/or on same strand, and those pairs are valid pairs. I want to use your function readGAlignmentPairs in GenomicRnages package to read  the pairs, but the manual says that it will discard those pairs. Do you have any suggestion?
>>
>> You could use readGAlignmentsList() instead of readGAlignmentPairs().
>> readGAlignmentsList() will keep these "discordant pairs". It will also
>> keep the reads that cannot be paired.
>> Note that, depending on what you will do downstream, you don't
>> necessarily need to pair the reads (e.g. if you're going to compute
>> the read coverage). In that case you can just load the reads with
>> readGAlignments().
>>
>> Cheers,
>> H.
>>
>>>
>>> Best,
>>> Liang
>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319