methylation: combine_neg option; oracle compares both background variants and logs sesame's negative controls

scripts/v2/sesame_oracle.R

@@ -32,6 +32,9 @@ for (prefix in args[-(1:3)]) {
     sesameDataCache("idatSignature")
     read()
   })
+  neg <- tryCatch(negControls(sdf), error = function(e) NULL)
+  cat("negative controls found by sesame:", if (is.null(neg)) "error" else nrow(neg), "\n")
+  print(head(sdf[grepl("^ctl", sdf$Probe_ID), ], 3))
   pv <- pOOBAH(sdf, return.pval = TRUE)
   sn <- noob(sdf)
   ib <- inband(sn)