WGCNA: matrixToNetwork – R documentation

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WGCNA

matrixToNetwork

Construct a network from a matrix

Description

Constructs a network

Usage

matrixToNetwork(
    mat, 
    symmetrizeMethod = c("average", "min", "max"), 
    signed = TRUE, 
    min = NULL, max = NULL, 
    power = 12,
    diagEntry = 1)

Arguments

`mat`	matrix to be turned into a network. Must be square.
`symmetrizeMethod`	method for symmetrizing the matrix. The method will be applied to each component of mat and its transpose.
`signed`	logical: should the resulting network be signed? Unsigned networks are constructed from `abs(mat)`.
`min`	minimum allowed value for `mat`. If `NULL`, the actual attained minimum of `mat` will be used. Missing data are ignored. Values below `min` are truncated to `min`.
`max`	maximum allowed value for `mat`. If `NULL`, the actual attained maximum of `mat` will be used. Missing data are ignored. Values below `max` are truncated to `max`.
`power`	the soft-thresholding power.
`diagEntry`	the value of the entries on the diagonal in the result. This is usally 1 but some applications may require a zero (or even NA) diagonal.

Details

If signed is FALSE, the matrix mat is first converted to its absolute value.

This function then symmetrizes the matrix using the symmetrizeMethod component-wise on mat and t(mat) (i.e., the transpose of mat).

In the next step, the symmetrized matrix is linearly scaled to the interval [0,1] using either min and max (each either supplied or determined from the matrix). Values outside of the [min, max] range are truncated to min or max.

Lastly, the adjacency is calculated by rasing the matrix to power. The diagonal of the result is set to diagEntry. Note that most WGCNA functions expect the diagonal of an adjacency matrix to be 1.

Value

The adjacency matrix that encodes the network.

Author(s)

Peter Langfelder