Entering edit mode
Ron,
Yes, you can use data$shortestestDistance<100000 to filter. Here is an
old post to address similar questions. Thanks!
https://stat.ethz.ch/pipermail/bioconductor/attachments/20110120/d5a5b
6be/attachment.pl
Best regards,
Julie
On 6/29/11 10:39 AM, "Ron Hart" <rhart@rci.rutgers.edu> wrote:
Thanks again, Julie, for the snippet you sent--worked perfectly to let
me add gene symbols to my output.
Ive got another question. Id like to limit the shortestDistance in
the ranged data object I use as input to getEnrichedGO. Im worried
that some of the peaks are quite far away from the TSSs and these may
be affecting the GO analysis. Im not clear on how to do this with
ranged data. Is there some equivalent to data$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
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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