proconaNet-class: proconaNet S4 class

In ProCoNA: Protein co-expression network analysis (ProCoNA).

Description

The main ProCoNA object - holder of data.

Objects from the Class

Objects can be created by calls of the form new(proconaNet ...)

Slots

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"

adj:

The adjacency matrix. "matrix"

TOM:

The topological overlap matrix or TOM. "matrix"

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"

Methods

show

signature(x = "proconaNet"): Shows info about the network.

print

signature(x = "proconaNet"): Prints info about the network.

Author(s)

David L Gibbs

ProCoNA documentation built on Nov. 1, 2018, 3:28 a.m.