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

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

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