Compute pairwise modification co-occurrence odds ratios.

Given a modkit mod_calls.tsv.gz file, build a per-read binary modification matrix for each tRNA and compute Fisher's exact test for each pair of positions. This is computationally expensive for full datasets; use the refs parameter to restrict to specific tRNAs.

Usage

compute_odds_ratios(mod_calls_path, refs = NULL, min_reads = 10)

Arguments

mod_calls_path

Path to a {sample}.mod_calls.tsv.gz file from modkit.

refs

Optional character vector of reference names to include. If NULL, all references are processed.

min_reads

Minimum number of reads required for a tRNA to be included. Default 10.

Value

A tibble with columns: ref, pos1, pos2, odds_ratio, log_odds_ratio, p_value, total_obs.