recoupHeatmap {recoup} | R Documentation |
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.
recoupHeatmap(recoupObj, samples = NULL, rc = NULL)
recoupObj |
a list object created from
|
samples |
which samples to plot. Either numeric
(denoting the sample indices) or sample ids. Defaults
to |
rc |
fraction (0-1) of cores to use in a multicore
system. It defaults to |
The function returns the recoupObj
with the
slot for the profile plot filled. See also the
recoupPlot
, getr
and setr
function.
Panagiotis Moulos
# 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)