recoupProfile {recoup} | R Documentation

## Plot (faceted) average genomic coverage profiles

### Description

This function takes as input argument and output object from `recoup` and creates the average genomic curve profiles according to 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

        recoupProfile(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.

### Author(s)

Panagiotis Moulos

### 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=0.1
    )

    # Plot coverage profiles
    recoupProfile(test.tss,rc=0.1)

[Package recoup version 1.18.0 Index]