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Last data update: 2014.03.03

R: Aggregate peaks over bins from the TSS

binOverFeature

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/binOverFeature.Rd_%03d_medium.png", width=480, height=480)
> ### Name: binOverFeature
> ### Title: Aggregate peaks over bins from the TSS
> ### Aliases: binOverFeature
> ### Keywords: misc
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>