recoup (version 1.0.2)

recoupHeatmap: Plot genomic coverage heatmaps

Description

This function takes as input argument and output object from recoup and creates heatmaps depicting genomic coverages using the ComplexHeatmap package and the options present in the input object. It can be used with saved recoup outputs so as to recreate the plots without re-reading BAM/BED files and re-calculating coverages.

Usage

recoupHeatmap(recoupObj, samples = NULL, rc = NULL)

Arguments

recoupObj

a list object created from recoup.

samples

which samples to plot. Either numeric (denoting the sample indices) or sample ids. Defaults to NULL for all samples.

rc

fraction (0-1) of cores to use in a multicore system. It defaults to NULL (no parallelization).

Value

• The function returns the recoupObj with the slot for the profile plot filled. See also the recoupPlot, getr and setr function.

Examples

# Load some data
data("recoup_test_data",package="recoup")

# Calculate coverages
test.tss <- recoup(
    test.input,
    design=NULL,
    region="tss",
    type="chipseq",
    genome=test.genome,
    flank=c(2000,2000),
    selector=NULL,
    plotParams=list(profile=FALSE,heatmap=FALSE),
    rc=0.5
)

# Plot coverage profiles
recoupHeatmap(test.tss,rc=0.5)