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]