plotGammaFit {lumi} | R Documentation |
gammaFitEM
plot the fitting results of gammaFitEM
. It basically plot the histogram of M-values plus the estimated gamma density plots and their mixture.
plotGammaFit(x, gammaFit = NULL, k = NULL, theta = NULL, shift = NULL, proportion = NULL, plotType = c("histogram", "density"), ...)
x |
a vector of M-values covering the whole genome |
gammaFit |
a "gammaFit" class object returned by |
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 |
This function is to visualize the fitting results, which helps us understand how well the fitting is.
Invisibly return TRUE if the plot is successful.
Pan DU
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)