[Bioc-devel] ShortRead: optional custom labeling of samples in QA report

[Martin Morgan]

On 02/12/2013 06:29 AM, Julian Gehring wrote:
> Hi,
>
> Since the attached file didn't make it all the way through to the mailing list,
> you can find it at
> http://www.ebi.ac.uk/~jgehring/share/shortRead-pkg/0001-Example-patch-for-naming-samples-in-BAMQA.patch.

Thanks Julian the request seems reasonable and I'll try to get to this in the 
next week. Martin

>
>
>
> Best wishes
> Julian
>
>
> On 02/12/2013 03:23 PM, Julian Gehring wrote:
>> Hi,
>>
>> In the QA report of the 'ShortRead' package, a short sequential integer
>> labeling for referencing the samples/files throughout the report is
>> created by default.  Would it be reasonable/possible to allow for other
>> optional names to label the samples to make the results of the report
>> easier to understand?
>>
>> In general, I have three ideas what would be handy to have:
>>
>> 1. Derive a label from the file names.  This is probably hard to
>> generalize and implement in a way that it actually helps.
>>
>> 2. In case the 'dirPath' argument in the 'qa' function call is a named
>> vector, such as
>>
>>      qa(dirPath=c(p1="bam_file1.bam", p2="bam_file2.bam"))
>>
>> use the names ["p1", "p2"] for the labeling later on.  This would
>> require storing the names in the object returned by 'qa', but should not
>> be too hard to implement.
>>
>> 3. Optionally, pass a named vector to the 'report' method, matching file
>> names to sample labels.  In case the file names do not match or
>> 'samples' is missing, default to the sequential labeling.
>>
>>
>> For option 3, I have created a simple example patch to illustrate how
>> this could be implemented (see attached).  So, later this may look like
>> this:
>>
>>
>>      library(ShortRead)
>>      files = c(p1="bam_file1.bam", p2="bam_file2.bam")
>>      qa = qa(files, type="BAM")
>>
>>      ## default sequential labeling ##
>>      ShortRead:::.report_html_BAMQA(qa, dest="report_normal")
>>
>>      ## samples named according to names(files) ##
>>      ShortRead:::.report_html_BAMQA(qa, dest="report_named", samples=files)
>>
>>
>> I'm happy about any inputs or thoughts regarding this.
>>
>>
>> Best wishes
>> Julian
>>
>>
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>>
>
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