summarizePeaks: summarizePeaks

In chromswitch: An R package to detect chromatin state switches from epigenomic data

Description

Given peaks for a set of samples in a query region, construct a sample-by- feature matrix where each row is a vector of summary statistics computed from peaks in the region.

Usage

summarizePeaks(localpeaks, mark, cols, fraction = TRUE, n = FALSE)

Arguments

localpeaks	LocalPeaks object
mark	String specifying the name of the mark for which the LocalPeaks object is given
cols	Character vector of column names on which to compute summary statistics
fraction	Loogical: compute the fraction of the region overlapped by peaks?
n	Logical: compute the number of peaks in the region?

Value

A matrix where rows are samples and columns are features

Examples

samples <- c("E068", "E071", "E074", "E101", "E102", "E110")
bedfiles <- system.file("extdata", paste0(samples, ".H3K4me3.bed"),
package = "chromswitch")

metadata <- data.frame(Sample = samples,
    H3K4me3 = bedfiles,
    stringsAsFactors = FALSE)

lpk <- retrievePeaks(H3K4me3,
    metadata = metadata,
    region = GRanges(seqnames = "chr19",
    ranges = IRanges(start = 54924104, end = 54929104)))

summarizePeaks(lpk, mark = "H3K4me3", cols = c("qValue", "signalValue"))

chromswitch documentation built on Nov. 8, 2020, 5:24 p.m.