nicolynnvila/splicing_epistasis_okgp_tcga_nondriver_recurrent

Splicing epistasis — Non-driver+TCGA-recurrent panel (Panel B)

94,984 cis-double SNV pairs (47,492 observed + 47,492 unobserved-matched) in 1000 Genomes across 663 genes that satisfy:

• —NOT in OncoKB cancerGeneList.tsv, AND
• —carry ≥2 TCGA-clean double-mutation pairs each with ≥5 carriers (per tcga_de_novo_pairs_clean.csv from the original paper-2 code dump)

Built as the non-driver arm of a three-panel strict test. These are genes that show recurrent doublet events in TCGA cancers but are not classified as cancer drivers.

Methodology

Same as paper §2 ¶1-5:

• —≤100 nt intra-gene window
• —≥3 1KG carriers per constituent
• —TopLD r² ≥ 0.2 dropped
• —Greedy 1:1 matched arms keyed on gene + log-rarity bin + distance ±2 nt
• —seed=42

Files

• —inputs.parquet — 94,984 matched-arm pairs
• —gene_panel.txt — the 663-gene list
• —stats.json — enumeration / matching counts