destroy_pattern: Destroy Phylotranscriptomic Pattern Using GATAI

Description

Apply the GATAI algorithm to identify and remove genes that contribute to phylotranscriptomic patterns.

Usage

destroy_pattern(
  phyex_set,
  num_runs = 20,
  runs_threshold = 0.5,
  analysis_dir = NULL,
  plot_results = TRUE,
  max_generations = 10000,
  seed = 1234,
  extended_analysis = FALSE,
  min_pval = 0.05,
  always_return_genes = FALSE,
  ...
)

Value

A list containing GATAI results including identified genes that contribute to the pattern

Arguments

phyex_set: A PhyloExpressionSet object (bulk or single cell, the latter which will get pseudo-bulked)
num_runs: Number of GATAI runs to perform (default: 20)
runs_threshold: Threshold for gene removal consistency across runs (default: 0.5)
analysis_dir: Directory to store GATAI analysis results (default: NULL)
plot_results: Whether to plot the results. If analysis dir is given, this will be ignored.
max_generations: Integer. Maximum number of generations (iterations) for the genetic algorithm (default 10000).
seed: Random seed for reproducibility (default: 1234)
extended_analysis: Whether to show the multiple runs and convergence plots (default: FALSE)
min_pval: Minimum p-value for which the pattern is considered destroyed (default: 0.05).
always_return_genes: Whether to return genes even when the pattern is not destroyed (default: FALSE).
...: Additional arguments passed to gataiR::gatai

Author

Filipa Martins Costa

Details

This function requires the gataiR package to be installed. GATAI systematically removes genes that contribute to phylotranscriptomic patterns by iteratively testing gene removal and evaluating the impact on the overall transcriptomic signature.