merge_results {ActivePathways} | R Documentation |
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")
)
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 |
Value
A list containing the merged results
Examples
## Not run:
# 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')
)
## End(Not run)
[Package ActivePathways version 2.0.6 Index]