Calculate pairwise co-occurrence of cytogenetic alterations

Computes Fisher's exact test for each pair of cytogenetic markers to identify significant co-occurrence or mutual exclusivity patterns.

Usage

calculate_cooccurrence(cyto_data, markers = NULL)

Arguments

cyto_data

Data frame from extract_cytogenetic_data()

markers

Character vector of marker columns. Default auto-detects.

Value

Data frame with columns: marker1, marker2, odds_ratio, pvalue, padj (BH-corrected), n_both, n_either, tendency (co-occurrence/exclusive/none)

See also

Other cytogenetics: compute_riss(), extract_cytogenetic_data(), plot_cooccurrence_heatmap(), plot_cytogenetic_oncoprint(), plot_expression_by_subtype(), summarize_cytogenetics()

Examples

if (FALSE) { # \dontrun{
cyto <- arrow::read_parquet("data/raw/clinical/cytogenetic_data.parquet")
cooc <- calculate_cooccurrence(cyto)
} # }