ActivePathways (version 2.0.6)

merge_gmt: Merge and filter GMT files based on a list of term IDs

Description

This function reads a GMT file and filters it to include only the specified term IDs. It's useful for creating a filtered GMT file for visualization in Cytoscape.

Usage

merge_gmt(gmt_file, term_ids)

Value

A GMT object containing only the specified terms

Arguments

gmt_file

Path to the GMT file

term_ids

Character vector of term IDs to include

Examples

if (FALSE) {
# Get term IDs from merged results
merged_results <- merge_results(
  enriched_pathways, enriched_pathways_directional,
  gmt_file = fname_GMT2,
  output_prefix = "Aggregated",
  tests = c('rna', 'protein', 'combined'),
  col_colors = c("#FF0000", "#00FF00", "#FFFFF0")
)

# Merge and filter GMT file
merge_gmt(
  gmt_file = fname_GMT2,
  term_ids = merged_results$term_ids
)
}