WGCNA: newNetworkOptions – R documentation

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WGCNA

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", "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