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 3.26.4 Index]