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

[Julian Gehring]

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.


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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>