find_modules: Co-expression modules definition

Description Usage Arguments Value Examples

Description

Defines co-expression modules

Usage

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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

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# 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))

CEMiTool documentation built on March 13, 2021, 2 a.m.