sesame oracle: compare without bead-count masking on both sides

scripts/v2/methyl_oracle_compare.py

@@ -36,7 +36,8 @@ def main() -> int:
     pos = {p: i for i, p in enumerate(man.probe_ids)}
     res = {}
     for prefix in a.prefixes:
-        s = sig.assemble(read_idat(prefix + "_Grn.idat"), read_idat(prefix + "_Red.idat"), man)
+        # min_beads=0: the oracle runs without bead-count masking (see sesame_oracle.R)
+        s = sig.assemble(read_idat(prefix + "_Grn.idat"), read_idat(prefix + "_Red.idat"), man, min_beads=0)
         p = sig.detection_p(s)
         n, fg, fr = sig.noob(s)
         b = sig.beta_values(n)

scripts/v2/sesame_oracle.R

@@ -24,7 +24,9 @@ inband <- function(s) {
   list(m = m, u = u)
 }
 for (prefix in args[-(1:3)]) {
-  read <- function() readIDATpair(prefix, platform = "EPIC", manifest = mft, controls = controls, min_beads = 3)
+  # no bead-count masking here (sesame's min_beads also masks every Infinium II probe, whose M address is NA);
+  # the comparison script runs simurg with the same setting
+  read <- function() readIDATpair(prefix, platform = "EPIC", manifest = mft, controls = controls)
   sdf <- tryCatch(read(), error = function(e) {
     message("first read failed (", conditionMessage(e), "); caching idatSignature and retrying")
     sesameDataCache("idatSignature")