printTopGenes {lemma}R Documentation

LEMMA - printing the most likely nonnull genes

Description

This program prints `topgenes' genes sorted in ascending order by their posterior null probability, or by their adjusted p-value. Use a positive integer, or `all' to print all the genes, or `nonnull' to print only the genes that are declared nonnull with the given local fdr or FDR cut-off values. It is executed by lemma(), but can be executed later separately, if the user wants to print a different number of `topgenes', without running the EM algorithm again.

Usage

  printTopGenes(type, outdir, data0, data1, data2, geneid, genename,
     topgenes, titletext, cutoff, modes)

Arguments

type Either `RR' or `FDR'.
outdir The directory with the AllData.RData file from a previous invocation of lemma(). The output files will be stored in the outdir directory (overwriting the previous copy).
data0 Enter RRfdr0 if type=`RR', or pBH0 if type=`FDR'
data1 Enter RRfdr1 if type=`RR', or (dg-tau) if type=`FDR'
data2 Enter (dg-tau) if type=`RR', or c() if type=`FDR'
geneid Use the geneid vector
genename Use the genename vector
topgenes the number of genes to print (sorted in ascending order by local-fdr or adjusted p-value). Use `all' to print all the genes, or `nonnull' to print only the genes that are declared nonnull with the given local fdr or FDR cut-off values. Default=`nonnull'.
titletext The title to be used in the output files.
cutoff Enter locfdrcutoff if type=`RR', or fdrcutoff if type=`FDR'
modes the number of assumed (null + nonnull) groups. Can be either 2 or 3 (default=3)

[Package lemma version 1.2-1 Index]