WGCNA: newConsensusOptions – R documentation

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newConsensusOptions

Create a list holding consensus calculation options.

Description

This function creates a list of class ConsensusOptions that holds options for consensus calculations. This list holds options for a single-level analysis.

Usage

newConsensusOptions(
      calibration = c("full quantile", "single quantile", "none"),

      # Simple quantile scaling options
      calibrationQuantile = 0.95,
      sampleForCalibration = TRUE, 
      sampleForCalibrationFactor = 1000,

      # Consensus definition
      consensusQuantile = 0,
      useMean = FALSE,
      setWeights = NULL,
      suppressNegativeResults = FALSE,
      # Name to prevent files clashes
      analysisName = "")

Arguments

`calibration`	Calibration method. One of `"full quantile", "single quantile", "none"` (or a unique abbreviation of one of them).
`calibrationQuantile`	if `calibration` is `"single quantile"`, input data to a consensus calculation will be scaled such that their `calibrationQuantile` quantiles will agree.
`sampleForCalibration`	if `TRUE`, calibration quantiles will be determined from a sample of network similarities. Note that using all data can double the memory footprint of the function and the function may fail.
`sampleForCalibrationFactor`	Determines the number of samples for calibration: the number is `1/calibrationQuantile * sampleForCalibrationFactor`. Should be set well above 1 to ensure accuracy of the sampled quantile.
`consensusQuantile`	Quantile at which consensus is to be defined. See details.
`useMean`	Logical: should the consensus be calculated using (weighted) mean rather than a quantile?
`setWeights`	Optional specification of weights when `useMean` is `TRUE`.
`suppressNegativeResults`	Logical: should negative consensus results be replaced by 0? In a typical network connstruction, negative topological overlap values may results with `TOMType = "signed Nowick"`.
`analysisName`	Optional character string naming the consensus analysis. Useful for identifying partial consensus calculation in hierarchical consensus analysis.

Value

A list of type ConsensusOptions that holds copies of the input arguments.

Author(s)

Peter Langfelder

WGCNA

Weighted Correlation Network Analysis

v1.70-3

GPL (>= 2)

Authors

Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang

Initial release

2021-02-17