data.4.toy.network: List containing the results from the application of the...
In FunctionalNetworks: An algorithm for gene and gene set network inference

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This dataset contains a list with the results from the application of the function data.generation for a toy dataset based on the breastCancerVDX dataset. It is based on the Molecular Functions ontology from GO by the MSigBD. Only MF with at least 5 genes were considered. See the package Vignette for a detailed usage.

1	data(data.4.toy.network)

A list containing the information in the following way:

gene.data A matrix with gene expression data. Rows are genes (HUGO ids) and columns are samples.
set.data A matrix with expression data for the gene sets. Rows are gene sets and columns are samples.
affy.loc A vector that contains the row numbers corresponding to the genes that are reported in the annotation system chosen
gene2set.mat A matrix that where each row represents a gene and each column contains the gene set to which this gene is reported based on the annotation system chosen.
set2gene.mat A matrix that where each row represents a gene set and each column contains the genes reported to be in the set based on the annotation system chosen.
Set.obj A vector with the gene sets set as objective nodes in the network.
Set.src A vector with the gene sets set as source nodes in the network.
G.obj A vector with the genes set as objective nodes in the network.
G.src A vector with the genes set as source nodes in the network.

This data set is calculated for the particular case were it is of interest to obtain the Functional Network for a toy dataset based on the breastCancerVDX dataset and the annotation system chosen is the MF from GO. The phenotype chose are the samples with Estrogen receptor negative (ER-).

A. Quiroz-Zarate. aquiroz@jimmy.harvard.edu

Quiroz-Zarate A, Haibe-Kains, B and Quackenbush J (2013). "Manuscript in preparation".