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 I’m using it for every ChIPseq dataset and finding beautiful GO associations and useful overlaps.

I’m 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 I’d 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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