diffPeakSummary: A function to identify and produce summary statistics for...

In Bioconductor/chipseq: chipseq: A package for analyzing chipseq data

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))

Bioconductor/chipseq documentation built on Oct. 29, 2023, 5:04 p.m.