binarizePeaks {chromswitch} | R Documentation

## binarizePeaks

### Description

Given peaks for a set of samples in a query region, construct a sample-by- feature matrix where each row is a binary vector which models the presence or absence of unqiue peaks in the region.

### Usage

    binarizePeaks(localpeaks, p)

### Arguments

`localpeaks` | LocalPeaks object storing peaks for all samples in the query region
`p` | Numeric value in [0, 1] giving the fraction of reciprocal overlap to require.

### Value

A data frame where rows are samples and columns are features. The genomic ranges which give the features are returned as the `features` attribute of the data frame.

### 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)))

    # Get feature matrix
    ft_matrix <- binarizePeaks(lpk, 0.5)

    # See features
    attr(ft_matrix, "features")

[Package chromswitch version 1.10.0 Index]