ora_data: Retrieve over representation analysis (ORA) results

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

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))

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