ora_data: Retrieve over representation analysis (ORA) results

Description Usage Arguments Details Value References Examples

Description

Retrieve over representation analysis (ORA) results

Usage

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ora_data(fc)

## S4 method for signature 'fcoex'
ora_data(fc)

Arguments

fc

Object of class fcoex

Details

This function returns the results of the mod_ora function on the fcoex 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.

This function was ipsis litteris adapted from the CEMiTool package.

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

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data("fc")
ora_data(fc)

csbl-usp/fcoex documentation built on Sept. 15, 2021, 7:42 a.m.