multiGSEA: Calculate pathway enrichment for multiple omics layer.

In yigbt/multiGSEA: Combining GSEA-based pathway enrichment with multi omics data integration

Calculate pathway enrichment for multiple omics layer.

Description

This function calculates GSEA-based enrichments scores for multiple omics layer at once. Input pathways or gene sets have to be prepared in advance by means of the function initOmicsDataStructure. The function uses pre- ranked lists for each omics layer to calculate the enrichment score. The ranking can be calculated by means of the function rankFeatures.

Usage

multiGSEA(pathways, ranks, eps = 0)

Arguments

pathways	Nested list containing all pathway features for the respective omics layer.
ranks	Nested list containing the measured and pre-ranked features for each omics layer.
eps	This parameter sets the boundary for calculating the p value.

Value

Nested list containing the enrichment scores for each given pathway and omics layer.

Examples

# Download pathway definition and extract features
pathways <- getMultiOmicsFeatures(dbs = c("kegg"), layer = c("transcriptome", "proteome"))

# load omics data and calculate ranks
data(transcriptome)
data(proteome)
ranks <- initOmicsDataStructure(c("transcriptome", "proteome"))
ranks$transcriptome <- rankFeatures(transcriptome$logFC, transcriptome$pValue)
names(ranks$transcriptome) <- transcriptome$Symbol
ranks$proteome <- rankFeatures(proteome$logFC, proteome$pValue)
names(ranks$proteome) <- proteome$Symbol

## run the enrichment
multiGSEA(pathways, ranks)

yigbt/multiGSEA documentation built on April 28, 2023, 10:02 p.m.