WGCNA (version 1.61)

newNetworkOptions: Create a list of network construction arguments (options).

Description

This function creates a reusable list of network calculation arguments/options.

Usage

newNetworkOptions(
    correlationOptions = newCorrelationOptions(),
    # Adjacency options
    replaceMissingAdjacencies = TRUE,
    power = 6,
    networkType = c("signed hybrid", "signed", "unsigned"),
    checkPower = TRUE,
    # Topological overlap options
    TOMType = c("signed", "unsigned", "none"),
    TOMDenom = c("mean", "min"))

Arguments

correlationOptions

A list of correlation options. See newCorrelationOptions.

replaceMissingAdjacencies

Logical: should missing adjacencies be replaced by zero?

power

Soft-thresholding power for network construction.

networkType

network type. Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See adjacency.

checkPower

Logicel: should the power be checked for sanity?

TOMType

One of "none", "unsigned", "signed". If "none", adjacency will be used for clustering. If "unsigned", the standard TOM will be used (more generally, TOM function will receive the adjacency as input). If "signed", TOM will keep track of the sign of correlations between neighbors.

TOMDenom

Character string specifying the TOM variant to be used. Recognized values are "min" giving the standard TOM described in Zhang and Horvath (2005), and "mean" in which the min function in the denominator is replaced by mean. The "mean" may produce better results but at this time should be considered experimental.

Value

A list of class NetworkOptions.

See Also

codenewCorrelationOptions