binOverFeature: Aggregate peaks over bins from the TSS

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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)

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.