plotGammaFit: plot the fitting results of 'gammaFitEM'

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

plot the fitting results of gammaFitEM. It basically plot the histogram of M-values plus the estimated gamma density plots and their mixture.

Usage

plotGammaFit(x, gammaFit = NULL, k = NULL, theta = NULL, shift = NULL, proportion = NULL, plotType = c("histogram", "density"), ...)

Arguments

x	a vector of M-values covering the whole genome
gammaFit	a "gammaFit" class object returned by gammaFitEM
k	parameter k of gamma distribution
theta	parameter theta of gamma distribution
shift	parameter shift of gamma distribution
proportion	the proportion of two components (gamma distributions)
plotType	determine the way to show the distribution of the input data, either histogram or density plot
...	Other parameters used by hist or plot (for "density" plotType) function.

Details

This function is to visualize the fitting results, which helps us understand how well the fitting is.

Value

Invisibly return TRUE if the plot is successful.

Author(s)

Pan DU

See Also

gammaFitEM

Examples

data(example.lumiMethy)
M <- exprs(example.lumiMethy)
fittedGamma <- gammaFitEM(M[,1], initialFit=NULL, maxIteration=50, tol=0.0001, plotMode=FALSE, verbose=FALSE)
plotGammaFit(M[,1], gammaFit=fittedGamma)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.