newConsensusOptions {WGCNA}

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