adj_data: Get or set adjacency matrix value

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

Get or set adjacency matrix value

Description

This function takes a CEMiTool object containing expression values and returns a CEMiTool object with an adjacency matrix in the adjacency slot.

Usage

adj_data(cem, ...)

## S4 method for signature 'CEMiTool'
adj_data(cem)

adj_data(cem) <- value

## S4 replacement method for signature 'CEMiTool'
adj_data(cem) <- value

Arguments

cem	Object of class CEMiTool
...	Optional parameters.
value	Object of class matrix containing adjacency data. Only used for setting adjacency values to CEMiTool object.

Value

Object of class matrix with adjacency values or object of class CEMiTool.

Examples

# Get example expression data
data(expr0)
# Initialize new CEMiTool object with expression
cem <- new_cem(expr0, filter=TRUE, apply_vst=FALSE)
# Calculate adjacency matrix with example beta value 8
cem <- get_adj(cem, beta=8)
# Return adjacency matrix
adj <- adj_data(cem)
# Check result
adj[1:5, 1:5]
# Set adjacency matrix to CEMiTool object
adj_data(cem) <- adj

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