Lucia,

Just to let you know that now you can specify output = "shortestDistance" in annotatePeakInBatch to get the output you specified.  The update is available in the dev version 2.11.5, but will be made available in the next release on April 14.

Thanks for your feedback!

Best regards,

Julie


On 3/20/14 6:26 PM, "Lihua Julie Zhu" <julie.zhu@umassmed.edu> wrote:

Lucia,

Yes, by default the function returns the gene with the shortest distance from peak start to TSS. You could try to set output = “both”, maxgap = 5000, PeakLocForDistance = “middle” to have the function output all genes that are within 5kb away from the middle of the peak. For detailed parameter setting, please type help(annotatePeakInBatch) in a R session.

Hope this helps.

Best regards,

Julie


On 3/20/14 4:11 PM, "Lucia Peixoto" <luciap@iscb.org> wrote:

Hi Julie,

I have run ChIPpeakAnno without any size constraints to see what happened.
It seemed to be running fine, but when I went to look at my positive controls I realized that it is not annotating all the intragenic peaks as "inside"

For example, I have a peak in
chr15 89378450 89379100 (mm9) and although it falls inside a gene it assigns it as upstream the gene right downstream from it.

Any idea what could be the problem? is it because I am using TSS as annotation file and this peak is closer to the TSS os the next gene eventhough it is still intragenic? is there anyway to keep this from happening and getting true intragenic calls?

Here is my R code:


myPeakList<-read.table ("DESonoseq_All.bed")
peakRange= BED2RangedData(myPeakList)
annotatedPeak = annotatePeakInBatch(peakRange, AnnotationData=TSS.mouse.NCBIM37)
as.data.frame(annotatedPeak)

thanks

Lucia






On Fri, Mar 7, 2014 at 2:56 PM, Zhu, Lihua (Julie) <Julie.Zhu@umassmed.edu> wrote:
Lucia,

If you type help(annotatePeakInBatch), you will see that there is a
parameter "output" with three options. By default, it is set to nearestStart
which will generate nearest features without any distance constraint. If you
set "output" to one of the other two options, then the distance cutoff can
be set by specifying "maxgap", e.g., 5000 as 5kb. Please let me know if this
answers your questions.

Best regards,

Julie


On 3/7/14 2:18 PM, "Lucia Peixoto" <luciap@iscb.org> wrote:

> Hi,
> This is my first time using the package, so maybe this is a naive question
> What is the distance cutoff used to find "nearest feature (gene, exon,
> miRNA,etc)"
> or there isn't any and I can filter on it after the mapping?
> thanks





	[[alternative HTML version deleted]]

