recoup_test_data

test.design

test.exons

test.genome

test.input

The testing data package containes a small gene set, a 
    design data frame, some genomic regions and an input 
    object for testing of recoup with ChIP-Seq and RNA-Seq 
    data. Specifically:
    <ul><li><code>test.input</code>: A small data set which 
        contains 10000 reads from H4K20me1 ChIP-Seq 
        data from WT adult mice and Set8 (Pr-Set7) KO 
        mice. The tissue is liver.</li><li><code>test.genome</code>: A small gene set (100 
        genes) and their coordinates from mouse mm9 
        chromosome 12.</li><li>test.design</li></ul>: A data frame containing the 100 
        above genes categorized according to expression and 
        strand.
        <item>test.exons</item>: A <code>GRangesList</code> containing 
        the exons of the 100 above genes for use with 
        <code>recoup</code> RNA-Seq mode.

datasets

recoup calculates and plots signal profiles
    created from short sequence reads derived from Next
    Generation Sequencing technologies. The profiles
    provided are either sumarized curve profiles or heatmap
    profiles. Currently, recoup supports genomic profile
    plots for reads derived from ChIP-Seq and RNA-Seq
    experiments. The package uses ggplot2 and ComplexHeatmap
    graphics facilities for curve and heatmap coverage
    profiles respectively.

Panagiotis Moulos

recoup

An R package for the creation of complex genomic
    profile plots

recoup_test_data function

<code>data.frame</code> and <code>list</code> objects whose format 
is accepted by recoup.

format

Personal communication with the Talianids lab at BSRC 
    'Alexander Fleming'. Unpublished data.

recoup_test_data: Reference and genomic sample regions for recoup testing

Description

Arguments

format

source