[R] using BLAT in r

[Uwe Ligges]

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
>