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
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?From=SE&Person=1134


On 8/11/14 9:03 AM, "Preussner, Jens" <Jens.Preussner@mpi-bn.mpg.de> 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)


	[[alternative HTML version deleted]]

