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

In WGCNA: Weighted Correlation Network Analysis

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", "signed Nowick", "unsigned", "none",
                "signed 2", "signed Nowick 2", "unsigned 2"),
    TOMDenom = c("mean", "min"),
    suppressTOMForZeroAdjacencies = FALSE,
    suppressNegativeTOM = FALSE,

    # Internal behavior options
    useInternalMatrixAlgebra = FALSE)

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", "signed Nowick", "unsigned 2", "signed 2" and "signed Nowick 2". If "none", adjacency will be used for clustering. See TOMsimilarityFromExpr for details.
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.
suppressTOMForZeroAdjacencies	logical: for those components that have zero adjacency, should TOM be set to zero as well?
suppressNegativeTOM	Logical: should the result be set to zero when negative? Negative TOM values can occur when TOMType is "signed Nowick".
useInternalMatrixAlgebra	logical: should internal implementation of matrix multiplication be used instead of R-provided BLAS? The internal implementation is slow and this option should only be used if one suspects a bug in R-provided BLAS.

Value

A list of class NetworkOptions.

Author(s)

Peter Langfelder

See Also

codenewCorrelationOptions

WGCNA documentation built on Jan. 22, 2023, 1:34 a.m.