simulateDatExpr5Modules: Simplified simulation of expression data

In WGCNA: Weighted Correlation Network Analysis

Simplified simulation of expression data

Description

This function provides a simplified interface to the expression data simulation, at the cost of considerably less flexibility.

Usage

simulateDatExpr5Modules(
  nGenes = 2000,
  colorLabels = c("turquoise", "blue", "brown", "yellow", "green"),
  simulateProportions = c(0.1, 0.08, 0.06, 0.04, 0.02),
  MEturquoise, MEblue, MEbrown, MEyellow, MEgreen,
  SDnoise = 1, backgroundCor = 0.3)

Arguments

nGenes	total number of genes to be simulated.
colorLabels	labels for simulated modules.
simulateProportions	a vector of length 5 giving proportions of the total number of genes to be placed in each individual module. The entries must be positive and sum to at most 1. If the sum is less than 1, the leftover genes will be simulated outside of modules.
MEturquoise	seed module eigengene for the first module.
MEblue	seed module eigengene for the second module.
MEbrown	seed module eigengene for the third module.
MEyellow	seed module eigengene for the fourth module.
MEgreen	seed module eigengene for the fifth module.
SDnoise	level of noise to be added to the simulated expressions.
backgroundCor	backgrond correlation. If non-zero, a component will be added to all genes such that the average correlation of otherwise unrelated genes will be backgroundCor.

Details

Roughly one-third of the genes are simulated with a negative correlation to their seed eigengene. See the functions simulateModule and simulateDatExpr for more details.

Value

A list with the following components:

datExpr	the simulated expression data in a data frame, with rows corresponding to samples and columns to genes.
truemodule	a vector with one entry per gene containing the simulated module membership.
datME	a data frame containing a copy of the input module eigengenes.

Author(s)

Steve Horvath and Peter Langfelder

See Also

simulateModule for simulation of individual modules;

simulateDatExpr for a more comprehensive data simulation interface.

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.