DeMAND (version 1.2.0)

demandClass: The demand class constructor

Description

This function generates demand class instances

Usage

demandClass(exp, anno, network, moa=NULL, KLD=NULL)

Arguments

exp

A N-by-M numeric matrix where the rows represent N probes (or genes) and the columns represent M samples.

anno

A N-by-2 character matrix where the rows represent probes or genes in the same order as the exp matrix. The first column must hold the probe id or gene name as appears in the exp matrix, and the second column should hold their corresponding names (e.g gene symbol) as appears in the network matrix

network

A K-by-L (L>1) character matrix containing K interactions. The 1st column and the 2nd column contain the names of the interacting genes. If the following columns include a column called "ppi" then genes connected by ppi will be used without estimating the residuals in the Brown correction method. The rest of the columns are used only to distinguish duplicates.

moa

Filled my the runDeMAND function. A data frame containing DeMAND MoA predictions (i.e. Gene, p-value, adjusted p-values)

KLD

Filled my the runDeMAND function. A matrix containing the interactions that were analysed, their KL-divergence, and the p-value associated with the divergenece

Value

Instance of class demand

Examples

## Load toy example
data(inputExample)
dobj <- demandClass(exp=bcellExp, anno=bcellAnno, network=bcellNetwork)
printDeMAND(dobj)