ora_data {CEMiTool} | R Documentation

## Retrieve over representation analysis (ORA) results

### Description

Retrieve over representation analysis (ORA) results

### Usage

    ora_data(cem)

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

### Arguments

`cem` | Object of class `CEMiTool`

### Details

This function returns the results of the `mod_ora` function on the `CEMiTool` object. The ID column corresponds to pathways in the gmt file for which genes in the modules were enriched. The Count column shows the number of genes in the module that are enriched for each pathway. The GeneRatio column shows the proportion of genes in the module enriched for a given pathway out of all the genes in the module enriched for any given pathway. The BgRatio column shows the proportion of genes in a given pathway out of all the genes in the gmt file. For more details, please refer to the `clusterProfiler` package documentation.

### Value

Object of class `data.frame` with ORA data

### References

Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

### 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 1.18.1 Index]