MAMA (version 2.2.1)

gene.select.FC: Function to select genes according to fold change

Description

Function selects genes with fold change (in absolute value) above input cutoff

Usage

gene.select.FC(fch, cutoff)

Arguments

fch

Data frame of fold change with columns corresponding to microarray experiments and rows to genes

cutoff

Cutoff for selection

Value

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")
#gene selection
genes.selected<-gene.select.FC(fch, 1)