[R] using BLAT in r

[Paul Hiemstra]

Fahim wrote:
> I am trying to use blat in R. I couldn't find any package in CRAN or
> bioconductor. I downloaded the windows executable from Jim Kent's (from
> ucsc) webpage. I was wondering how to use/call these executables or
> functions embedded in these executables. 
> I am seeking for some direction or some material that addresses such
> problem.
> Help appreciated. 
> Thanks
>
> -Fahim Mohammad 
> cecs, univ of Louisville    
>   
Hi Fahim,

The easiest way I can see is to use system() to call the executable. 
Probably BLAT uses some text parameter files to specify what it needs to 
do. Write an R function that generates the BLAT parameters files, run 
BLAT and process the result using another function, something like this:

writeParameterfile()
system(blat)
getOutcomes()

Another option, a hard one though, is to link the source code of BLAT 
directly into R. But I think using system is a good alternative.

cheers,
Paul

-- 
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul
http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770