binOverFeature {ChIPpeakAnno} | R Documentation

## 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.

### Author(s)

Jianhong Ou

### 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)

[Package ChIPpeakAnno version 3.22.4 Index]