[BioC] biomaRt getFeature function
Paul.Hammer at p-t-p.de
Tue Nov 18 17:11:53 CET 2008
I've installed the package biomaRt currently and I tried to use the
function "getFeature". But I had to notice that this function does not
exist. So since what time is that function removed from the package and
is there now a comparable function?
By the way I try to get out following. I have a lot of dna fragments. I
know from every fragment the location on the genome (chromosom, start
and end base position). Now I would like to know if a fragment is
located directly in a gene (that would be easy with the getFeature
function from biomaRt :) ). If a fragment is not located in a gene I
would like to get out which and where the next gene is located upstream
and downstream. Normally I would code a simple perl script which would
compare the fragment positions with the annotated cDNA positions but I
want to do it in R because all my other analysis I've done also in R.
Maybe somebody knows a easy trick to solve my question...
Thanks in advance,
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