demand-instance: The DeMAND instance

Description Arguments

Description

This instance stores parameters and results of theDeMAND algorithm

Arguments

exp

A N by M numeric matrix and the rows are N probes and the columns are M samples.

anno

A N by 2 character matrix. The rows are probes but the order should be the same with the demand matrix. The first column can be anything (usually probe IDs) but the second column should includes Official Gene Symbol information for each probe.

network

A K by 4 character matrix which contains K interactions. The 1st column and the 2nd column contain pairs of interacted genes. The 3rd and 4th columns indicate whether the interactions are pr otein-protein interaction (ppi) or protein-DNA (pdi) interaction. Column name should be as follows: c("Gene1", "Gene2", "ppi", "pdi")

moa

A data frame contains DeMAND MoA predictions (e.g. Gene, p-value, adjusted p-values)

KLD

A matrix containing the KL-divergence of the interactions that were analysed, the KL-divergence that was evaluated, and the p-value associated with the divergenece



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