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, ptm.correlation.matrix)

Arguments

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 igraph edgelist object.
2 The gene CoCluster Correlation Network as an igraph edgelist object. 3 (PTM CoCluster Correlation Network) A matrix that shows the strength of the relationships between PTMs using the common clusters between the three distance metrics
4 (Gene CoCluster Correlation Network) Similar to 1 but at the level of genes.

Examples

Example_Output <- MakeCorrelationNetwork(ex_adj_consensus, ex.ptm.correlation.matrix)
#> [1] "Making PTM CCCN"
#> Error in ptm.cccn[active_ptms, active_ptms, drop = FALSE]: incorrect number of dimensions
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