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]