After Annotation in R , the binding sites are less than the starting downloaded from ENCODE Chip-seq Matrix

Question

[atsalaki]

I download ENCODE chip-seq broadpeak files and annotate them in R with annotatePeakInBatch(gr_narrowPeak, featureType = c("TSS"),maxgap=5000 ,AnnotationData=annotationData , output="overlapping", FeatureLocForDistance="TSS") .The binding sites i get are less that the starting in the ENCODE peak files (e.g i had 40.000 and after the annotation i get only 14.000 ). Can anyone explain to me why this is happening?

[Friederike]

Can you provide the results of the following code:

str(gr_narrowPeak)
str(annotatePeakInBatch(gr_narrowPeak, featureType = c("TSS"),maxgap=5000 ,AnnotationData=annotationData , output="overlapping", FeatureLocForDistance="TSS") ))