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
>
>


-- 
Lucia Peixoto PhD
Postdoctoral Research Fellow
Laboratory of Dr. Ted Abel
Department of Biology
School of Arts and Sciences
University of Pennsylvania

"Think boldly, don't be afraid of making mistakes, don't miss small
details, keep your eyes open, and be modest in everything except your
aims."
Albert Szent-Gyorgyi

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