CreateNetworkMatrix: Create network matrix by using the cancer-specific genes
In cosmonet-package/COSMONET: Screening-network Cox methods for survival analysis

This function creates a network matrix with zero diagonal and non-negative off-diagonal used to calculate Laplacian matrix and of dimention pxp. Since this is a cancer-specific study, the tissue-specific network has been downloaded. The example below is done with the top-edges Network file using the files available at https://hb.flatironinstitute.org/download.

CreateNetworkMatrix(
  x,
  repositoryDisease,
  diseaseID = NULL,
  topGenes = NULL,
  tissueSpecificEdge,
  output = TRUE,
  message = TRUE
)

`x`	input matrix `nxp`. Each row is an observation vector.
`repositoryDisease`	the repository disease is a repository where the prediction score associated to each gene is a posterior probability. The higher the probability the stronger the functional relation between the gene and the cancer.
`diseaseID`	the disease ID from disease ontology (http://disease-ontology.org).
`topGenes`	the number of the top functional genes associated with the disease.
`tissueSpecificEdge`	file downloaded from https://hb.flatironinstitute.org/download. Top Edges: the network is filtered to only include edges with evidence supporting a tissue-specific functional interaction. [entrez gene id 1][entrez gene id 2][posterior prob.]
`output`	if TRUE the Omega matrix is saved as .txt file in the current directory.
`message`	if TRUE returns a message showing the number of edges in the graph.

The following objects are returned:

`DiseaseGenes`	top cancer-disease genes and relative posterior probabilities.
`Omega`	network matrix with zero diagonal and non-negative off-diagonal `pxp`.