OmicGsea

Geneset Enrichment Analysis for Complex Omics Data

Introduction

The Bioconductor R package OmicGsea provides gene set enrichment analysis functions for complex Omics data. In many omics datasets, such as Illumina DNA methylation data, genes are often represented by variable numbers of correlated probes, and a single probe may map to multiple genes. This complex data structure poses significant challenges for gene set enrichment analysis. The OmicGsea package addresses these challenges by providing both threshold- and ranking-based competitive enrichment analysis methods, effectively accounting for probe correlation and probe number bias. These versatile functions can be applied to a wide range of omics datasets, including DNA methylation, proteomics, genotyping, and genome sequencing. Additionally, the package includes a fast and accurate ranking-based enrichment method specifically designed for gene expression and RNA-seq data.

Functions

• `gseaGene()`: Gene set enrichment analysis based on gene level combined p-values
• `gseaPG()`: Gene set enrichment analysis based on combined probe group p-values
• `gseaProbe()`: Gene set enrichment analysis based on probe level p-values
• `gseaRank()`: Ranking-based set enrichment analysis based on gene level p-values