Entering edit mode
Ron,
Thanks for the positive feedback and the suggestions!
Description field is included in the annotation. You can add the
description field in the annotatedPeak by merging the annotatedPeak
with the annotation file.
AP = as.data.frame(your.annotatedPeak)
AN = as.data.frame(TSS.human.NCBI37) ##### The annotation data used
for annotating your peaks.
X =merge(AP, AN, by.x= c("feature", "start_position", "end_position",
"strand", "space"), by.y= c("names", "start", "end", "strand",
"space"), all.x=TRUE)
I could add a parameter AttributeFields in getAnnotation function for
users to specify additional fields such as hgnc_symbol to be obtained
from biomaRt.
Best regards,
Julie
On 6/23/11 4:45 PM, "Ron Hart" <rhart@rci.rutgers.edu> wrote:
Hi Julie,
Thanks for providing the very valuable ChIPpeakAnno package. I find
Im using it for every ChIPseq dataset and finding beautiful GO
associations and useful overlaps.
Im wondering if there was a way to extract a little more information
from biomaRt during the peak annotation step. You provide the
ensemble_gene_id field already, but Id like to have the hgnc_symbol
and maybe the description fields. Is there a way to pass a parameter
to annotatePeakInBatch to do this? Maybe a list of the attribute
fields desired?
Thanks again,
Ron
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