[BioC] rTANDEM package -- An R encapsulation of the X!Tandem algorithm

[Steve Lianoglou]

Hi Frederic,

On Wed, Dec 19, 2012 at 10:36 AM, Frederic Fournier
<frederic.bioinfo at gmail.com> wrote:
> Dear Bioconductor users,
>
> I would like to announce the release of the new package rTANDEM on
> bioconductor.
> This package encapsulates the mass spectrometry indentification algorithm
> X!Tandem in R, making it possible to conduct a full ms-ms analysis in R and
> to use R datamining capacities to search the results. We hope that rTANDEM
> can become the center of a viable pipeline for ms-ms proteomics in R.
>
> Questions, suggestions, bug-reports, and feedback of any kind is more than
> welcome.

Really cool!

Thanks for putting this together ... I checked out the source code to
skim the package and notice that you use data.table (good choice :-) I
see, however, that you felt that you needed to resort to some hacks to
get it to work correctly, for instance in `GetPeptides`, you have:

  ## Dummy declaration to prevent "no visible binding" note when using
data.table subset:
  pep.id=prot.uid=uid=NULL
  rm(pep.id, prot.uid, uid)
  ...

But this shouldn't be necessary, so if there's a problem in data.table
I'd like to fix it.

I'm curious if you list data.table in your "Imports" field in your
DESCRIPTION file, then `import(data.table)` in your NAMESPACE, is this
still necessary?

I don't think I've run into this problem before, so I'm hoping these
small changes should do the trick.

HTH,
-steve
-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact