summarizePeaks {chromswitch} | R Documentation

## summarizePeaks

### 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"))

[Package chromswitch version 1.8.0 Index]