If this is the mail tools called blat: I use it with shell() calls all
the time even for sending out automatical notifications for the CFAN
build service.
Note that there is also the "sendmailR" package gthat can send out
messages without need for some additional 3rd party software...
Uwe Ligges
On 11.04.2010 11:44, Paul Hiemstra wrote:
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
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