mod_ora: Module Overrepresentation Analysis

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

Module Overrepresentation Analysis

Description

Performs overrepresentation analysis for each co-expression module found.

Usage

mod_ora(cem, ...)

## S4 method for signature 'CEMiTool'
mod_ora(cem, gmt, verbose = FALSE)

Arguments

cem	Object of class CEMiTool.
...	Optional parameters.
gmt	Object of class data.frame with 2 columns, one with pathways and one with genes
verbose	logical. Report analysis steps.

Value

Object of class CEMiTool

See Also

ora_data

Examples

# Get example CEMiTool object
data(cem)
# Read gmt file
gmt <- read_gmt(system.file('extdata', 'pathways.gmt',
                   package='CEMiTool'))
# Run module overrepresentation analysis
cem <- mod_ora(cem, gmt)
# Check results
head(ora_data(cem))

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