diffPeakSummary {chipseq} | R Documentation

## A function to identify and produce summary statistics for differentially expressed peaks.

### Description

Given two sets of peaks, this function combines them and summarizes the individual coverage vectors under the combined peak set.

### Usage

    diffPeakSummary(ranges1, ranges2,
                    viewSummary = list(sums = viewSums, maxs = viewMaxs))

### Arguments

`ranges1` | First set of peaks (typically an `RleViewsList`).
`ranges2` | Second set of peaks (typically an `RleViewsList`).
`viewSummary` | A list of the per peak summary functions.

### Value

A `data.frame` with one row for each peak in the combined data. The chromosome, start and stop nucleotide positions (+ strand) are given as are the summary statistics requested.

### Author(s)

D. Sarkar

### Examples

    data(cstest)
    library(BSgenome.Mmusculus.UCSC.mm9)
    seqlevels(cstest) <- seqlevels(Mmusculus)
    seqlengths(cstest) <- seqlengths(Mmusculus)
    ## find peaks
    findPeaks <- function(reads) {
      reads.ext <- resize(reads, width = 200)
      slice(coverage(reads.ext), lower = 8)
    }
    peakSummary <- diffPeakSummary(findPeaks(cstest$gfp), findPeaks(cstest$ctcf))

[Package chipseq version 1.42.0 Index]