demand-instance

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

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

anno

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")

network

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

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


This instance stores parameters and results of theDeMAND algorithm


DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.

Jung Hoon Woo

DeMAND

demand-instance function

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

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")

This instance stores parameters and results of theDeMAND algorithm

demand-instance: The DeMAND instance

Description

Arguments