lemmaPlots {lemma}R Documentation

LEMMA - diagnostics plots

Description

This program produces two diagnostics plots for the two fitting procedures in the LEMMA model.

Usage

 lemmaPlots(outdir, mgq=0.99, titletext, modes) 

Arguments

outdir The directory containing the RData file with the saved estimates and data from a previous invocation of lemma(). Default=‘OUT’
mgq The quantile used for plotting the m_g histogram. Genes with m_g values outside the mgq quantile are excluded from the plot. Default=0.99
titletext The title of the plot
modes The number of assumed (null + nonnull) groups. Can be either 2 or 3 (default=3).

Details

The function lemmaPlots generates two plots on one page, and saves them in postscript and pdf formats under the outdir directory.

(a) a histogram of the d_g statistics and the fitted curves for the null and nonnull groups, as well as the mixture (using the average error variance).

(b) a histogram of m_g, and the fitted distribution, based on the estimates for alpha and beta.

Note - we are using ps2pdf to convert the postscript format to pdf. It is assumed to be installed on the computer.


[Package lemma version 1.2-1 Index]