MAMA (version 2.1.0)

fold.change: Function to do compute fold change between two groups

Description

Function computes fold change between two groups of log2-transformed data

Usage

fold.change(x, varname)

Arguments

x

MetaArray object

varname

Character String specifying which column of clinical data matrices should be used as class labels. Column of this name must be present in each clinical data matrix.

Value

• Data frame of fold changes, each column refer to one study and row to genes.

Examples

#data preparation
data(Singhdata)
cl1<-as.data.frame(Singhdata$classes[[1]])
names(cl1)<-"classlab"
cl2<-as.data.frame(Singhdata$classes[[2]])
names(cl2)<-"classlab"
cl3<-as.data.frame(Singhdata$classes[[3]])
names(cl3)<-"classlab"

rownames(Singhdata$esets[[1]])<-Singhdata$geneNames
rownames(Singhdata$esets[[2]])<-Singhdata$geneNames
rownames(Singhdata$esets[[3]])<-Singhdata$geneNames

dataset<-new("MetaArray", GEDM=list(Singhdata$esets[[1]], Singhdata$esets[[2]], Singhdata$esets[[3]]),
clinical=list(cl1, cl2, cl3), datanames=c("dataset1", "dataset2", "dataset3"))

#fold change
fch<-fold.change(dataset, "classlab")
head(fch)