twoA	as.matrix	c	cbind	data	eBayes	Egambia	head	library	lmFit	rep	topTable
basic2	c	E	Egambia	rep	showGene
mod1	<	>	$	&	abs	tmodHGtest	tt
mod2	$	head	nrow	tmodUtest	tt
fourB	$	head	tmodCERNOtest	tt
five	evidencePlot	l
limma1	$	Egambia	fit	head	length	names	tmodLimmaTest
limma2	>	$	abs	c	fit	head	length	max	min	order	par	plot	print	segments	T	tmodLimmaTopTable
limma3	$	abs	Egambia	fit	head	order	T	tmodCERNOtest	tmodLimmaTopTable
pplot0	head	res.l	tmodSummary
pplot1	res.l	tmodPanelPlot
pplot2	$	data	Egambia	fit	head	order	T	tmod	tmodLimmaDecideTests
pplot3	pie	res.l	tmodPanelPlot
pplot4	pie	res.l	tmodPanelPlot
pplot5	[[	$	cbind	Egambia	fit	identical	pie	tmodDecideTests	topTable
fiveB	$	head	tmodUtest	tt
six	$	as.character	c	E	group	legend	library	par	pca2d	prcomp	t
seven	$	abs	Egambia	head	order	pca	tmodUtest
pcasum	$	abs	apply	Egambia	order	pca	T	tmodCERNOtest	tmodSummary
pcsum2	tmodPanelPlot	x
pcsum3	$	apply	gs	pca	quantile	tmodDecideTests	tmodPanelPlot	x
eight	$	library	log10	res	smoothPalette	strmultline	tagcloud
nine	$	abs	as.character	c	Egambia	group	layout	legend	log10	matrix	mypal	order	par	pca	pca2d	smoothPalette	strmultline	tagcloud	tags	tmodUtest	w
nineB	$	Egambia	group	list	mypal	pca	tmodPCA
perm1	$	eBayes	lmFit	ncol	order	require	sample	topTable
perm2	$	as.matrix	c	cbind	dim	Egambia	permset	rep	sapply	set.seed	tmodAUC
perm3	==	>=	$	$<-	all	c	design	E	eBayes	Egambia	head	lmFit	N	order	p.adjust	pauc	perms	rownames	sapply	sum	T	tmodCERNOtest	topTable
ten	[[	$	data	geneSetTest	sapply	tmod	tmodUtest	tt
eleven	$	abline	gst	plot	res
exmset	c	data.frame	list	makeTmod
msigdbparse1	tmodImportMSigDB
msigdb6	$	head	msig	tmodCERNOtest	tt
msigdb7	==	$	msig	tmodCERNOtest	tt
msigdb1	library	xmlParse	xmlToList
msigdb2	[[	class	foo2
msigdb2b	names	path1
msigdb3	==	!	foo2	is.null	sapply	unique
msigdb4	c	colnames<-	data.frame	foo3	sapply	t
msigdb5	[[	$	foo3	lapply	makeTmod	modules	names<-	strsplit
wpex1	$	$<-	download.file	gsub	T	tempfile	unzip
wpex2	$	as.character	files	human	library	ls	mget	names<-	org.Hs.egSYMBOL	read.csv	sapply	suppressMessages	unique	unlist	unz
wpex3	>	$	$<-	data.frame	files	length	p2GENES	paste0	rownames<-	sapply
wpex4	makeTmod	p2GENES	pathways
wpex5	$	Hspaths	tmodCERNOtest	tt
wpex6	$	grep	Hspaths	T	tmodCERNOtest	tt
metabodata	data	factor	gsub	rownames	table	tbmprof
metabowilcoxon	~	$	apply	c	colnames	data.frame	sapply	t	T	tbmprof	wilcox.test
metabo01	$	c	modmetabo
metabopanelplot	res	tmodPanelPlot
metabopie	$	c	colnames<-	modmetabo	res	tmodDecideTests	tmodPanelPlot	wcx
metabowilcoxontmod	$	$<-	list	modmetabo	order	tmodCERNOtest	wcx
metabosex	$	c	modmetabo	order	par	sex	showGene	showModule	tb	tbmprof
pplot2.5	all	names	pie	res.l
nineC	$	Egambia	pca	plot	print	tmodPCA
tmodpca	colnames	list	modmetabo	prcomp	T	tb	tbmprof	tmodPCA
tmodpca3	$	ret	tmodPanelPlot
tmodpca4	colnames	list	modmetabo	prcomp	T	tb	tbmprof	tmodPCA
tmodpca5	~	$	c	head	lm	order	sapply	summary	t
tmodpca6	c	colnames	list	modmetabo	paste	pca	sex	tb	tbmprof	tmodPCA
