Re: ChIPpeakAnno: Maxgap option in annotatePeakInBatch

Dear Jens,

Thanks for the feedback!

Maxgap does not appply when output = nearestStart, which is the default setting. Maxgap applies when you set output = overlapping, as shown below.

annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=10)
annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=40)
annotatePeakInBatch(a, AnnotationData = g, output="overlapping", maxgap=400)

For more options to call annotatePeakInBatch, please type ?annotatePeakInBatch in a R session.

I am ccing bioconductor list so others with similar questions can benefit.

Best regards,

Julie


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program in Gene Function and Expression
Program in Bioinformatics and Integrative Biology
Program in Molecular Medicine
University of Massachusetts Medical School
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On 8/11/14 9:03 AM, "Preussner, Jens" <Jens.Preussner-6GLbxAiBP3Zo1qOY/[email protected]> wrote:

Dear Julie,

I have some issues with the maxgap option when using the annotatePeakInBatch function of your ChIPpeakAnno package in R.
It seems that the maxgap option is ignored. Suppose I have two bed files, the first one defining a peak between 1050 and 1100 on chr1, the latter defining a gene from 500 to 1000, also on chr1. Running annotatePeakInBatch with maxgap=40 still returns the interval.
Please find attached two files, a.bed and g.bed, and the corresponding R code that I used to run it.

Thank you for a short answer,
Best,
Jens

Jens Preußner
Bioinformatics Service
Max Planck Institute for Heart and Lung Research
Ludwigstrasse 43 – FGI –
61231 Bad Nauheim
Germany

R-Code:
require('ChIPpeakAnno')
a = BED2RangedData(file.path("a.bed"))
g = BED2RangedData(file.path("g.bed"))
annotatePeakInBatch(a, AnnotationData = g, maxgap=10)
annotatePeakInBatch(a, AnnotationData = g, maxgap=40)


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