extractPvalues: Create a reshaped data frame from multiGSEA output.

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

Create a reshaped data frame from multiGSEA output.

Description

This function reshapes the output from multiGSEA to get a single data frame with columns for p-values and adjusted p-values for each omics layer. Each row of the data frame represents one pathway.

Usage

extractPvalues(enrichmentScores, pathwayNames)

Arguments

enrichmentScores	Nested List of enrichment scores, calculated by multiGSEA function.
pathwayNames	List containing Pathway names.

Value

Data frame where rows are pathways and columns are (adjusted) p-values for each 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
es <- multiGSEA(pathways, ranks)

extractPvalues(
  enrichmentScores = es,
  pathwayNames = names(pathways[[1]])
)

yigbt/multiGSEA documentation built on Oct. 31, 2024, 2:22 p.m.