Added random seed as variable

scripts/prepare_BRCA.R

@@ -16,6 +16,7 @@ OUTROOT <- DATADIR
 tumor <- "Breast"
 targets <- list(ER="clin:breast_carcinoma_estrogen_receptor_status", subtypes="clin:PAM50Call")
 task <- "ER"
+base.seed <- 78 # use 78 to (re)generate the "main" set of splits
 
 # task-independent: generate a merged file from available omics layers
 mergedFile <- file.path(OUTROOT, tumor, "merged.txt")
@@ -77,8 +78,7 @@ foreach(split.id=seq(0, 9), .verbose=FALSE) %dopar% {
     outdir <- file.path(OUTROOT, tumor, "INF", ifelse(task=="ER", "breast_ER", task), split.id)
     if(!dir.exists(outdir))
         dir.create(outdir, recursive=TRUE)    
-    # make it so that the 1st split is for set.seed(78), which was the one created previously
-    set.seed(78+split.id)
+    set.seed(base.seed+split.id)
     train.idx <- caret::createDataPartition(y=y, p=0.7, list=FALSE)
     train.data <- mrg.sub[train.idx,]
     train.lab <- y[train.idx]