get_merged_mods: Merge similar modules

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

Merge similar modules

Description

This function takes a CEMiTool object with expression and a vector of numeric labels to merge similar modules.

Usage

get_merged_mods(cem, ...)

## S4 method for signature 'CEMiTool'
get_merged_mods(cem, mods, diss_thresh = 0.8, verbose = FALSE)

Arguments

cem	Object of class CEMiTool.
...	Optional parameters.
mods	A vector containing numeric labels for each module gene
diss_thresh	A threshold of dissimilarity for modules. Default is 0.8.
verbose	Logical. If TRUE, reports analysis steps. Default FALSE

Value

Numeric labels assigning genes to modules.

Examples

# Get example expression data
data(expr0)
# Initialize new CEMiTool object with expression data
cem <- new_cem(expr0, filter=TRUE, apply_vst=FALSE)
# Calculate adjacency matrix with example beta value 8
cem <- get_adj(cem, beta=8)
# Get modules
mods <- get_mods(cem)
# Merge similar modules
merged_mods <- get_merged_mods(cem, mods)

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