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Make Correlation Network

Source: R/MakeCorrelationNetwork.R
MakeCorrelationNetwork.Rd

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.

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
#> PTM CCCN complete after 0.28 secs total.
#> Making Gene CCCN
#> Gene CCCN complete after 2.79 secs total.
head(Example_Output[[1]])
#>                                                                              source
#> 1                                                                       SHC1 p S426
#> 2                                                                        PXN p S119
#> 3                                                                      PRKCD p S304
#> 4                                                                       CTTN p S417
#> 5                                                                      SRSF9 p S178
#> 6 HSP90AA1 p S63; HSP90AA2P p S63; HSP90AB1 p S58; HSP90AB3P p S58; HSP90AB2P p S58
#>            target     Weight          interaction
#> 1      SYK p S295 -1.0000000 negative correlation
#> 2   ANXA11 p S480 -0.7642857 negative correlation
#> 3     CTTN p S447  0.7000000 positive correlation
#> 4     CTTN p S418  1.0000000 positive correlation
#> 5      SHB p S247 -1.0000000 negative correlation
#> 6 HSP90AB4P p S34  1.0000000 positive correlation
head(Example_Output[[2]])
#>   source target     Weight          interaction
#> 1 ADGRL2  ALDOA -0.4535714          correlation
#> 2   ACP1    ALK  0.6000000 positive correlation
#> 3  AHNAK   ANO1  1.5428571 positive correlation
#> 4   ACP1  ANXA2 -0.2571429          correlation
#> 5 ADAM10  ANXA2  0.1702786          correlation
#> 6  ALDOA  ANXA2 -0.7524510 negative correlation