[Bioc-devel] ShortRead: optional custom labeling of samples in QA report
julian.gehring at embl.de
Tue Feb 12 15:29:34 CET 2013
Since the attached file didn't make it all the way through to the
mailing list, you can find it at
On 02/12/2013 03:23 PM, Julian Gehring wrote:
> 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
> 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
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