Make Correlation Network

Make Correlation Network filters a correlation matrix of PTMs by specific PTMs. It groups the PTM correlation matrix based on the Genes of PTMs. By summing these submatrices, it also produces a gene by gene cocluster correlation network shows strength of relationships between proteins using the common clusters between the three distance metrics.

Usage

MakeCorrelationNetwork(adj.consensus.matrix, ptm.correlation.matrix)

Arguments

adj.consensus.matrix

Adjacency matrix showing PTM co-cluster relationships from all three t-SNE embeddings

ptm.correlation.matrix

A data frame showing the correlation between ptms (as the rows and the columns). NAs are placed along the diagonal.

common.clusters

A list of clusters. Ideally the ones found by MakeClusterList in common_clusters

Value

A list containing the following data structures at the given index:

1. The PTM CoCluster Correlation Network as an edgelist.

2. The Gene CoCluster Correlation Network as an edgelist.

3. A list of nodes that are in the Gene CoCluster Correlation Network.

Examples

Example_Output <- MakeCorrelationNetwork(ex_adj_consensus, ex.ptm.correlation.matrix)
#> Making PTM CCCN
#> Error: object 'ex.ptm.correlation.matrix' not found
Example_Output[[1]][1:5, 1:5]
#> Error: object 'Example_Output' not found
Example_Output[[2]][1:5, 1:5]
#> Error: object 'Example_Output' not found