multiGSEA: Calculate pathway enrichment for multiple omics layer.

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

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)

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.

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)

multiGSEA documentation built on Nov. 8, 2020, 8:15 p.m.