change the name of the new option to isLowMemLOCO

saigegit · Jul 10, 2022 · 64d5433 · 64d5433
1 parent 51e9d4e
commit 64d5433
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/extdata/step1_fitNULLGLMM.R b/extdata/step1_fitNULLGLMM.R
@@ -55,8 +55,8 @@ option_list <- list(
    help="Optional. Initial values for tau. [default=0,0]"),
   make_option("--LOCO", type="logical", default=TRUE,
     help="Whether to apply the leave-one-chromosome-out (LOCO) approach when fitting the null model using the full GRM [default=TRUE]."),
-  make_option("--isOutputSepbyChr", type="logical", default=FALSE,
-    help="Whehter to output the model file by chromosome when LOCO=TRUE [default=FALSE]"),
+  make_option("--isLowMemLOCO", type="logical", default=FALSE,
+    help="Whehter to output the model file by chromosome when LOCO=TRUE. If TRUE, the memory usage in Step 1 and Step 2 will be lower [default=FALSE]"),
   make_option("--traceCVcutoff", type="numeric", default=0.0025,
     help="Optional. Threshold for coefficient of variation (CV) for the trace estimator. Number of runs for trace estimation will be increased until the CV is below the threshold [default=0.0025]."),
   make_option("--nrun", type="numeric", default=30,
@@ -226,7 +226,7 @@ fitNULLGLMM(plinkFile=opt$plinkFile,
             memoryChunk = opt$memoryChunk,
             tauInit = tauInit,
             LOCO = opt$LOCO,
-	    outputSepbyChr = opt$isOutputSepbyChr,
+	    isLowMemLOCO = opt$isLowMemLOCO,
             traceCVcutoff = opt$traceCVcutoff,
 	    nrun = opt$nrun,
             ratioCVcutoff = opt$ratioCVcutoff,