get_beta_data: Soft-threshold beta data

In csbl-usp/CEMiTool: Co-expression Modules identification Tool

Soft-threshold beta data

Description

This function takes the input parameters from find_modules and calculates the WGCNA soft-threshold parameters and returns them.

Usage

get_beta_data(cem, ...)

## S4 method for signature 'CEMiTool'
get_beta_data(
  cem,
  network_type = "unsigned",
  cor_function = "cor",
  cor_method = "pearson",
  verbose = FALSE
)

Arguments

cem	A CEMiTool object containing expression data
...	Optional parameters.
network_type	A character string indicating to use either "unsigned" (default) or "signed" networks. Default "unsigned".
cor_function	A character string indicating the correlation function to be used. Default 'cor'.
cor_method	A character string indicating which correlation coefficient is to be computed. Default "pearson"
verbose	Logical. If TRUE, reports analysis steps. Default FALSE

Value

A list containing the soft-threshold selected by WGCNA and scale-free model parameters

Examples

# Get example expression data
data(expr0)
# Initialize new CEMiTool object with expression data
cem <- new_cem(expr0, filter=TRUE, apply_vst=FALSE)
# Get beta data
beta_data <- get_beta_data(cem)

csbl-usp/CEMiTool documentation built on March 27, 2024, 5:14 a.m.