testOneGraph: Applies a serie of two-sample tests to each connected...

In DEGraph: Two-sample tests on a graph

Description

Applies a serie of two-sample tests to each connected component of a graph using various statistics.

Usage

testOneGraph(graph, data, classes, useInteractionSigns=TRUE, ..., verbose=FALSE)

Arguments

graph	A graph object.
data	A 'matrix' (size: number 'p' of genes x number 'n' of samples) of gene expression.
classes	A 'vector' (length: 'n') of class assignments.
useInteractionSigns	A logical value indicating whether the sign of interaction should be taken into account.
...	Further arguments to be passed to testOneConnectedComponent.
verbose	If TRUE, extra information is output.

Value

A structured list containing the p-values of the tests, the graph object of the connected component and the number of retained Fourier dimensions.

Author(s)

Laurent Jacob, Pierre Neuvial and Sandrine Dudoit

See Also

testOneConnectedComponent()

Examples

library("Rgraphviz")
library("KEGGgraph")
## library("NCIgraph")

data("Loi2008_DEGraphVignette")
exprData <- exprLoi2008
classData <- classLoi2008
annData <- annLoi2008

rn <- rownames(exprData)

## Retrieve expression levels data for genes from one KEGG pathway
graph <- grListKEGG[[1]]
pname <- attr(graph, "label")
print(pname)

## DEGraph T2 test
resList <- testOneGraph(graph, exprData, classData, verbose=TRUE, prop=0.2)

## Largest connected component
res <- resList[[1]]
gr <- res$graph

## individual t statistics
shift <- apply(exprData, 1, FUN=function(x) {
  tt <- t.test(x[classData==0], x[classData==1])
  tt$statistic
})
names(shift) <- translateGeneID2KEGGID(names(shift))

## color palette
if (require(marray)) {
  pal <- maPalette(low="red", high="green", mid="black", k=100)
} else {
  pal <- heat.colors(100)
}

## plot results
dn <- getDisplayName(gr, shortLabel=TRUE)
mm <- match(translateKEGGID2GeneID(nodes(gr)), rownames(annData))
dn <- annData[mm, "NCBI.gene.symbol"]
 
pvg <- plotValuedGraph(gr, values=shift, nodeLabels=dn, qMax=0.95, colorPalette=pal, height=40, lwd=1, verbose=TRUE, cex=0.5)
title(pname)

txt1 <- sprintf("p(T2)=%s", signif(res$p.value[1], 2))
txt2 <- sprintf("p(T2F[%s])=%s", res$k, signif(res$p.value[2]))
txt <- paste(txt1, txt2, sep="\n")
stext(side=3, pos=1, txt)
if (require(fields)) {
  image.plot(legend.only=TRUE, zlim=range(pvg$breaks), col=pal, legend.shrink=0.3, legend.width=0.8, legend.lab="t-scores", legend.mar=3.3)
}

DEGraph documentation built on Nov. 8, 2020, 5:52 p.m.