get_adj: Calculate adjacency matrix

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

Calculate adjacency matrix

Description

This function takes a CEMiTool object and returns an adjacency matrix.

Usage

get_adj(cem, ...)

## S4 method for signature 'CEMiTool'
get_adj(
  cem,
  beta,
  network_type = "unsigned",
  cor_function = "cor",
  cor_method = "pearson"
)

Arguments

cem	Object of class CEMiTool
...	Optional parameters.
beta	Selected soft-threshold value
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".

Value

Object of class CEMiTool with adjacency data

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)
# Check results
adj <- adj_data(cem)
adj[1:5, 1:5]

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