Compare using Rank Products (full matrix approach) — compare_pairwise

Rank Products requires ranking across ALL peptides simultaneously, not within single peptides. This function handles the matrix-based approach using the RankProd package.

Usage

compare_pairwise_rankprod(data, compare, ref, alpha, fdr_method)

Arguments

data: pepdiff_data object
compare: Factor to compare
ref: Reference level
alpha: Significance threshold
fdr_method: FDR correction method

Value

List with results and diagnostics tibbles