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Make Correlation Network

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(
  common.clusters,
  ptm.correlation.matrix,
  ptm.cccn.name = "ptm.cccn",
  gene.cccn.name = "gene.cccn"
)

Arguments

common.clusters

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

ptm.correlation.matrix

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

ptm.cccn.name

Desired name of the PTM correlation matrix filtered by specific PTMs from input

gene.cccn.name

Desired name for the cocluster correlation network; defaults to gene.cccn

Value

The list of common clusters between all three distance metrics (Euclidean, Spearman, and SED) and a matrix showing strength of relationships between proteins using the common clusters between the three distance metrics (Euclidean, Spearman, and Combined (SED))

Examples

ex.ptm.cor <- ex.ptm.correlation.matrix
MakeCorrelationNetwork(ex.common.clusters, ex.ptm.cor, "ex.ptm.cccn", "ex.gene.cccn")

ex.ptm.cccn[1:5, 1:5]
#>               ABLIM1 p Y357 ABLIM1 p Y373 MET p Y1003 PKP4 p Y1156
#> ABLIM1 p Y357            NA     0.8857143   0.8186275    0.8846154
#> ABLIM1 p Y373     0.8857143            NA   0.8637363    0.8637363
#> MET p Y1003       0.8186275     0.8637363          NA    0.6835165
#> PKP4 p Y1156      0.8846154     0.8637363   0.6835165           NA
#> ABLIM1 p Y383     0.6428571     0.8000000   0.9000000    0.3000000
#>               ABLIM1 p Y383
#> ABLIM1 p Y357     0.6428571
#> ABLIM1 p Y373     0.8000000
#> MET p Y1003       0.9000000
#> PKP4 p Y1156      0.3000000
#> ABLIM1 p Y383            NA
ex.gene.cccn[1:5, 1:5]
#>          ABLIM1       MET      PKP4      MYH9   SEC16A
#> ABLIM1       NA  44.48902  82.79735  36.05673 21.02892
#> MET    44.48902        NA 110.88877  66.78124 24.29454
#> PKP4   82.79735 110.88877        NA 221.19493 77.65545
#> MYH9   36.05673  66.78124 221.19493        NA 22.81430
#> SEC16A 21.02892  24.29454  77.65545  22.81430       NA