Skip to contents

Compare method concordance for differential analysis results

Source: R/s4_functions_concordance.R
calculate_concordance.Rd

Compares statistical results from two different methods (typically SAIT/GAM for continuous data and Conover-Iman Rank Transform tests) to assess agreement and identify genes detected by one method but not the other.

Usage

calculate_concordance(analysis_sait, analysis_rank = NULL, ...)

# S4 method for class 'TSENATAnalysis'
calculate_concordance(
  analysis_sait,
  analysis_rank = NULL,
  verbose = FALSE,
  output_file = NULL,
  ...
)

Arguments

analysis_sait

TSENATAnalysis object containing SAIT/GAM analysis results (from calculate_sait()).

analysis_rank

TSENATAnalysis object or NULL. If NULL, uses legacy single-object API with analysis_sait containing both results. If provided, compares SAIT results from analysis_sait with rank-test results from analysis_rank.

...

Additional arguments for future extensibility.

verbose

logical. Print progress messages (default: FALSE).

output_file

character or NULL. Optional file path to save results. Supported formats: .rds (for S4 objects). Default: NULL (no file output).

Value

Modified TSENATAnalysis object with concordance results stored in: @metadata$method_concordance:

comparison_df

Data frame comparing results from both methods

spearman_rho

Spearman correlation between adjusted p-values

high_confidence

Genes with strong agreement

agreement_table

Contingency table of significant/non-significant calls

sait_method

Method name used for SAIT/GAM analysis

rank_method

Method name used for rank-based analysis

timestamp

When concordance was computed

Details

Compares results from two different statistical methods (typically GAM for continuous and Conover-Iman Rank Transform for rank-based analysis) on the same data. Identifies: - Genes significant in both methods (high confidence) - Genes detected by one method only (potential false positives or method-specific signal) - Spearman correlation of p-values (overall agreement trends)

Examples

# Compare results from SAIT and rank-based testing
# (Requires pre-computed analysis objects from calculate_sait and calculate_rank_transform)
# results_df <- results(calculate_concordance(analysis_sait, analysis_rank))