adjust_export_pathway: Adjust and Export Pathway Analysis Results

In TransProR: Analysis and Visualization of Multi-Omics Data

Adjust and Export Pathway Analysis Results

Description

This function processes a dataframe containing fgsea results. It adjusts pathway names by removing underscores, converting to lowercase, then capitalizing the first letter, and joining the components with spaces. It selects and merges the top upregulated and downregulated pathways based on enrichment score (ES) and p-value.

Usage

adjust_export_pathway(fgseaRes, nTop = 10)

Arguments

fgseaRes	Dataframe containing fgsea results with columns 'pathway', 'ES', and 'pval'.
nTop	Integer, number of top pathways to select based on the p-value.

Value

A vector containing combined top upregulated and downregulated pathways.

Examples

# Create a synthetic fgseaRes dataframe
fgseaRes <- data.frame(
 pathway = c("KEGG_APOPTOSIS",
             "GO_CELL_CYCLE",
             "REACTOME_DNA_REPAIR",
             "KEGG_METABOLISM",
             "GO_TRANSPORT"),
 ES = c(0.45, -0.22, 0.56, -0.35, 0.33),
 pval = c(0.001, 0.02, 0.0003, 0.05, 0.01)
)

# Run the function to get top pathways
result <- adjust_export_pathway(fgseaRes = fgseaRes, nTop = 2)

TransProR documentation built on April 4, 2025, 3:16 a.m.