From 64d5433d6e67ec632e894f5d4738fa2f5c552030 Mon Sep 17 00:00:00 2001 From: saigegit Date: Sun, 10 Jul 2022 00:27:34 -0400 Subject: [PATCH] change the name of the new option to isLowMemLOCO --- extdata/step1_fitNULLGLMM.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/extdata/step1_fitNULLGLMM.R b/extdata/step1_fitNULLGLMM.R index 862c7442..f161b264 100644 --- 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,