find_modules: Co-expression modules definition

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

Co-expression modules definition

Description

Defines co-expression modules

Usage

find_modules(cem, ...)

## S4 method for signature 'CEMiTool'
find_modules(
  cem,
  cor_method = c("pearson", "spearman"),
  cor_function = "cor",
  eps = 0.1,
  set_beta = NULL,
  force_beta = FALSE,
  min_ngen = 20,
  merge_similar = TRUE,
  network_type = "unsigned",
  tom_type = "signed",
  diss_thresh = 0.8,
  verbose = FALSE
)

Arguments

cem	Object of class CEMiTool.
...	Optional parameters.
cor_method	A character string indicating which correlation coefficient is to be computed. Default "pearson"
cor_function	A character string indicating the correlation function to be used. Default 'cor'.
eps	A value for accepted R-squared interval between subsequent beta values. Default is 0.1.
set_beta	A value to override the automatically selected beta value. Default is NULL.
force_beta	Whether or not to automatically force a beta value based on number of samples. Default is FALSE.
min_ngen	Minimal number of genes per submodule. Default 20.
merge_similar	Logical. If TRUE, (the default) merge similar modules.
network_type	A character string indicating to use either "unsigned" (default) or "signed" networks. Default "unsigned"
tom_type	A character string indicating to use either "unsigned" or "signed" (default) TOM similarity measure.
diss_thresh	Module merging correlation threshold for eigengene similarity. Default 0.8.
verbose	Logical. If TRUE, reports analysis steps. Default FALSE

Value

Object of class CEMiTool

Examples

# Get example expression data
data(expr0)
# Initialize CEMiTool object with expression
cem <- new_cem(expr0, filter=TRUE, apply_vst=FALSE)
# Define network modules
cem <- find_modules(cem)
# Check results
head(module_genes(cem))

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