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,
...
)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