[BioC] retrieveGenomicFeatureAnnotation.R file supplied with Ringo

Paul Geeleher paulgeeleher at gmail.com
Thu Mar 4 13:10:25 CET 2010


I've been following the instructions in the Ringo manual and using
this file to associate my Chip Enriched regions with genomic features.
Thing is it seems that in retrieveGenomicFeatureAnnotation.R biomaRt
is querying the HG19 genome build. I haven't been able to find a way
of changing this to HG18, having searched the web I don't think it's
possible? If there is no way of explicitly specifying the genome build
maybe it would be worth noting somewhere in the file or documentation
that biomaRt is using HG19? Just that I guess the fast majority of
people will be using microarrays based on HG18?

As an alternative I think I'm just going to try reading gene locations
from a BED file on the UCSC site.



Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland

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