make.dex.set.object: Make a list object for function agdex()

Description

This function generates a list object containing four components for function agdex()

Usage

make.dex.set.object(Eset.data, comp.var, comp.def, gset.collection)

Arguments

Eset.data

an ExpressionSet object carries the gene expression data (Exprs) and Phenotype data (pData)

comp.var

the column name or numeric index for group labels in pData of object Eset.data

comp.def

a string definition of comparison, group labels connected by "-"

gset.collection

an object belongs to class GeneSetCollection

Value

A list object containing the four components described in argument section.

Details

The ExpressionSet includes two components: exprs: a matrix of expression values pData: a data frame contains the sample IDs and their assigned group labels.

gset.collection contains a GeneSetCollection object defined in the Bioconductor package GSEABase. The gset.collection object must use the same identifiers for probe-sets as that used in the exprs component of Eset.data.

Examples

Run this code

 # load data
 data(human.data)
 data(mouse.data) 
 data(gset.data)                  
 # make dex.set object for human data
 dex.set.human <- make.dex.set.object(human.data,
                                      comp.var=2,
                                      comp.def="human.tumor.typeD-other.human.tumors",
                                      gset.collection=gset.data)
 # make dex.set object for mouse data
 dex.set.mouse <- make.dex.set.object(mouse.data,
                                      comp.var=2,
                                      comp.def="mouse.tumor-mouse.control",
                                      gset.collection=NULL)

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