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
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