ActivePathways (version 2.0.6)

merge_results: Merge results from multiple ActivePathways analyses

Description

This function combines results from multiple ActivePathways analyses into a single set of files for visualization in Cytoscape. This is particularly useful for comparing results with and without directional penalties.

Usage

merge_results(
  enriched_pathways,
  enriched_pathways_directional,
  gmt_file,
  output_prefix = "Aggregated",
  col_colors = NULL,
  tests = c(gsub("^Genes_", "", grep("^Genes_", colnames(enriched_pathways), value =
    TRUE)), "combined")
)

Value

A list containing the merged results

Arguments

enriched_pathways

A data.table returned by ActivePathways

enriched_pathways_directional

A data.table returned by ActivePathways

gmt_file

Path to GMT file

output_prefix

A string prefix for output files

col_colors

A character vector of colors for each test (must match length of tests)

tests

A character vector of names for the data sources (e.g., c('rna', 'protein', 'combined')) or NULL

Examples

if (FALSE) {
# Run two different ActivePathways analyses
enriched_pathways <- ActivePathways(
  pval_matrix, gmt = fname_GMT2, cytoscape_file_tag = "original_")

enriched_pathways_directional <- ActivePathways(
  pval_matrix, gmt = fname_GMT2, cytoscape_file_tag = "directional_",
  merge_method = "DPM", scores_direction = dir_matrix, 
  constraints_vector = constraints_vector)

# Merge the results
merge_results(
  enriched_pathways, enriched_pathways_directional,
  gmt_file = fname_GMT2,
  output_prefix = "Aggregated",
  col_colors = c("#FF0000", "#00FF00", "#FFFFF0"),
  tests = c('rna', 'protein', 'combined')
)
}