ChIPpeakAnno (version 3.6.5)

binOverFeature: Aggregate peaks over bins from the TSS

Description

Aggregate peaks over bins from the feature sites.

Usage

binOverFeature(..., annotationData=GRanges(), select=c("all", "nearest"), radius=5000L, nbins=50L, minGeneLen=1L, aroundGene=FALSE, mbins=nbins,  featureSite=c("FeatureStart", "FeatureEnd", "bothEnd"), PeakLocForDistance=c("all", "end","start","middle"),  FUN=sum, errFun=sd, xlab, ylab, main)

Arguments

...

Objects of GRanges to be analyzed

annotationData

An object of GRanges or annoGR for annotation

select

Logical: annotate the peaks to all features or the nearest one

radius

The radius of the longest distance to feature site

nbins

The number of bins

minGeneLen

The minimal gene length

aroundGene

Logical: count peaks around features or a given site of the features. Default = FALSE

mbins

if aroundGene set as TRUE, the number of bins intra-feature. The value will be normalized by value * (radius/genelen) * (mbins/nbins)

featureSite

which site of features should be used for distance calculation

PeakLocForDistance

which site of peaks should be used for distance calculation

FUN

the function to be used for score calculation

errFun

the function to be used for errorbar calculation or values for the errorbar.

xlab

titles for each x axis

ylab

titles for each y axis

main

overall titles for each plot

Value

A data.frame with bin values.

Examples

bed <- system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno")
gr1 <- toGRanges(bed, format="BED", header=FALSE)
data(TSS.human.GRCh37)
binOverFeature(gr1, annotationData=TSS.human.GRCh37,
               radius=5000, nbins=10, FUN=length, errFun=0)