refactor: add p-value and correlation coefficient thresholds to AF time correlation rule

Author: ahmig

workflow/rules/vaf.smk

@@ -286,6 +286,8 @@ rule af_time_correlation_data:
     params:
         cor_method=config["COR"]["METHOD"],
         cor_exact=config["COR"]["EXACT"],
+        max_p_adj_threshold = 0.05,
+        min_abs_cor_threshold = 0.0,
     input:
         variants=OUTDIR / f"{OUTPUT_NAME}.variants.all_sites.tsv",
         metadata=config["METADATA"],

workflow/scripts/report/af_time_correlation_data.R

@@ -111,7 +111,10 @@ write_csv(
 
 log_info("Selecting variants whose allele frequency is significantly correlated with time")
 significant.variants <- correlations %>%
-  filter(p.value.adj < 0.05) %>%
+  filter(
+    p.value.adj <= snakemake@params$max_p_adj_threshold,
+    abs(coefficient) >= snakemake@params$min_abs_cor_threshold
+  ) %>%
   pull(variant) %>%
   unique()