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List:       bioc-devel
Subject:    Re: [Bioc-devel] ShortRead: optional custom labeling of samples in QA report
From:       Martin Morgan <mtmorgan () fhcrc ! org>
Date:       2013-02-12 14:37:00
Message-ID: 511A538C.9050801 () fhcrc ! org
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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
> > 
> > 
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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