cnv.plot: Plots posterior probabilty distributions

In CNVtools: A package to test genetic association with CNV data

Description

Makes formatted density plots from the posterior data frame(s) returned by CNVtest.binary

Usage

cnv.plot(posterior, hist.or.dens='histogram', batch = NULL, freq = NULL, ...)

Arguments

posterior	The posterior distribution obtained from the CNVtools fitting algorithm, for example using CNVtest.binary
hist.or.dens	Either 'histogram' or 'density' to plot the data as an histogram or using a kernel density estimator
batch	character vector (usually of length 1, but not always), designing the batches one wants to plot.
freq	This argument is only relevant when hist.or.dens='histogram' (the default). It matches the argument freq of the hist function. With freq = FALSE frequencies, and not raw counts, are shown in the histogram.
...	Usual arguments passed to the hist function, including main or breaks for example.

Author(s)

Vincent Plagnol [e-mail] and Chris Barnes [e-mail]

Examples

	#Load data for CNV for two control cohorts 
	data(A112)
	raw.signal <- as.matrix(A112[, -c(1,2)])
	dimnames(raw.signal)[[1]] <- A112$subject

	#Extract CNV signal using principal components
	pca.signal <- apply.pca(raw.signal)

	#Extract batch, sample and trait information
 	batches <- factor(A112$cohort)
	sample <- factor(A112$subject)
	trait <- ifelse( A112$cohort == '58C', 0, 1)

	#Fit the CNV with a three component model
	fit.pca <- CNVtest.binary(signal = pca.signal, sample = sample, batch = batches, 
		   	          disease.status = trait, ncomp = 3, n.H0=3, n.H1=3,
				  model.disease = "~ cn")
	
	cnv.plot(fit.pca[['posterior.H0']], batch = '58C', breaks = 30)			  	
		  

Example output

Loading required package: survival
Attempting to cluster the data with 2593 individuals and 3 components
Iteration 1 under H0
Iteration 2 under H0
Iteration 3 under H0
Iteration 1 under H1
Iteration 2 under H1
Iteration 3 under H1

CNVtools documentation built on April 28, 2020, 6:06 p.m.