get_mods: Calculate co-expression modules

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

Calculate co-expression modules

Description

This function takes a CEMiTool object containing an adjacency matrix together with the given network parameters, and returns the given co-expression modules.

Usage

get_mods(cem, ...)

## S4 method for signature 'CEMiTool'
get_mods(
  cem,
  cor_function = "cor",
  cor_method = "pearson",
  tom_type = "signed",
  min_ngen = 20
)

Arguments

cem	Object of class CEMiTool.
...	Optional parameters.
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".
tom_type	A character string indicating to use either "unsigned" or "signed" (default) TOM similarity measure.
min_ngen	Minimal number of genes per module (Default: 20).

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 module labels
mods <- get_mods(cem)

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