Ron,

Yes, you can use data$shortestestDistance<100000 to filter. Here is an old post to address similar questions. Thanks!
https://stat.ethz.ch/pipermail/bioconductor/attachments/20110120/d5a5b6be/attachment.pl

Best regards,

Julie


On 6/29/11 10:39 AM, "Ron Hart" <rhart@rci.rutgers.edu> wrote:

Thanks again, Julie, for the snippet you sent--worked perfectly to let me add gene symbols to my output.

I’ve got another question.  I’d like to limit the shortestDistance in the ranged data object I use as input to getEnrichedGO.  I’m worried that some of the peaks are quite far away from the TSS’s and these may be affecting the GO analysis.  I’m not clear on how to do this with ranged data.  Is there some equivalent to data$shortestDistance < 100000 that I can use to limit the peak list object?

Ron


From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu]
Sent: Friday, June 24, 2011 12:30 PM
To: Ron Hart
Cc: bioconductor
Subject: Re: choice of biomaRt feature from annotatePeakInBatch

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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