mod_ora {CEMiTool} | R Documentation

## 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`

### 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))

[Package CEMiTool version 1.0.3 Index]