Accessors {ProCoNA} | R Documentation

## Accessors for the proconaNet S4 class

### Description

Accessor functions allow access to the object data.

### Methods

`TOM`:

  The topological overlap matrix or TOM. `"matrix"`

`adj`:

  The adjacency matrix. `"matrix"`

`networkName`:

  A name describing the data or experiment used to build the network. `"character"`

`samples`:

  The names of samples used in building the network. `"character"`

`peptides`:

  The names of peptides used in the network, also the node names. `"character"`

`pepTree`:

  The network dendrogram. `"hclust"`

`dynamicColors`:

  The module labels on each node (or peptide). `"numeric"`

`MEs`:

  The module eigenvectors (or eigen-peptides). `"data.frame"`

`mergedMEs`:

  The module eigenvectors after merging similar modules. `"data.frame"`

`mergedColors`:

  The module labels after merging similar modules. `"numeric"`

`colorOrder`:

  Modules are ordered by size, these labels correspond to that order. `"character"`

`power`:

  The soft thresholding power used in scaling the adjacency matrix. `"numeric"`

`networkType`:

  Either a signed or unsigned network regarding the method used in computing the initial correlations between nodes. `"character"`

`permtest`:

  The results of the permutation test on signficance of topological overlap within modules. `"matrix"`

`proconaVersion`:

  Returns the version number of the software that built the object. `"character"`

### Author(s)

David L Gibbs

### Examples

    data(ProCoNA_Data)
    tomMatrix <- TOM(net1)

[Package ProCoNA version 1.18.0 Index]