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

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Description

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

Usage

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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

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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))