MAMA (version 2.2.1)

mergedata: Function to merge data from MetaArray object

Description

Function merges the data stored in MetaArray object. It binds expression data matrices into one gene expression data matrix. It creates one binary vector of class labels of the samples and one numeric vector of orgin of the samples.

Usage

mergedata(x, varname)

Arguments

x

MetaArray objec

varname

character String specifying the column of clinical data to be used in vector of class labels of the samples

Value

A list with three slots

dat

Gene expression data matrix, rows refer to genes/probes and columns to samples

cl

Binary vector of class labels of the samples

origin

Numeric vector describing the origin of the samples. Same number refers to samples from one study

Examples

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

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

merged.data<-mergedata(data,"classlab")
summary(merged.data)