merge_gmt {ActivePathways} | R Documentation |
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)
Arguments
gmt_file |
Path to the GMT file |
term_ids |
Character vector of term IDs to include |
Value
A GMT object containing only the specified terms
Examples
## Not run:
# 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
)
## End(Not run)
[Package ActivePathways version 2.0.6 Index]