[BioC] biomaRt getFeature function

Paul Hammer Paul.Hammer at p-t-p.de
Tue Nov 18 17:19:14 CET 2008

Dear folks,

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,

 > sessionInfo()
R version 2.8.0 (2008-10-20)


attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] brainwaver_1.4       waveslim_1.6.1       exonmap_2.0.0
 [4] RMySQL_0.6-1         DBI_0.2-4            RColorBrewer_1.0-2
 [7] genefilter_1.20.0    survival_2.34-1      biomaRt_1.16.0
[10] affy_1.18.1          preprocessCore_1.2.1 affyio_1.8.0
[13] HELP_1.0.0           Biobase_2.0.1

loaded via a namespace (and not attached):
[1] annotate_1.18.0     AnnotationDbi_1.2.1 RCurl_0.91-0
[4] RSQLite_0.7-0       XML_1.98-1

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