setting default to not remove phenotype outliers as we assume the use…

…r has taken steps to account for outliers in the phenotype data
jeffersonfparil · Jun 23, 2024 · e36bd00 · e36bd00
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commit e36bd00
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Showing 2 changed files with 1 addition and 13 deletions.
diff --git a/inst/exec_Rscript/config.txt b/inst/exec_Rscript/config.txt
@@ -1,15 +1,3 @@
-GENOTYPE_DATA_RDS=/group/pasture/Jeff/gp/inst/exec_Rscript/input_tmp/test_geno.Rds
-PHENOTYPE_DATA_TSV=/group/pasture/Jeff/gp/inst/exec_Rscript/input_tmp/test_pheno.tsv
-KFOLDS=3
-NREPS=3
-DIR_OUT=/group/pasture/Jeff/gp/inst/exec_Rscript/output_tmp
-SBATCH --job-name="AAA"
-SBATCH --account="dbiopast1"
-SBATCH --ntasks=1
-SBATCH --cpus-per-task=8
-SBATCH --mem=64G
-SBATCH --time=0-2:0:00
-
 GENOTYPE_DATA_RDS=${DIR_SRC}/input/test_geno.Rds
 PHENOTYPE_DATA_TSV=${DIR_SRC}/input/test_pheno.tsv
 KFOLDS=2

diff --git a/inst/exec_Rscript/gp.R b/inst/exec_Rscript/gp.R
@@ -27,7 +27,7 @@ parser$add_argument("--pheno-idx-col-id",                                dest="p
 parser$add_argument("--pheno-idx-col-pop",                               dest="pheno_idx_col_pop",                               type="integer", default=2,                                                                         help="Column number in the phenotype file corresponding to the population/grouping names [default=2].")
 parser$add_argument("--pheno-idx-col-y",                                 dest="pheno_idx_col_y",                                 type="integer", default=3,                                                                         help="Column number in the phenotype file corresponding to the numeric phenotype data [default=3].")
 parser$add_argument("--pheno-na-strings",                                dest="pheno_na_strings",                                type="character", default=c("", "-", "NA", "na", "NaN", "missing", "MISSING"),                     help="Strings of characters corresponding to missing data in the phenotype file [default=c('', '-', 'NA', 'na', 'NaN', 'missing', 'MISSING')].")
-parser$add_argument("--pheno-bool-remove-outliers",                      dest="pheno_bool_remove_outliers",                      type="logical", default=TRUE,                                                                      help="Remove outliers from the phenotype file [default=TRUE]?")
+parser$add_argument("--pheno-bool-remove-outliers",                      dest="pheno_bool_remove_outliers",                      type="logical", default=FALSE,                                                                      help="Remove outliers from the phenotype file [default=TRUE]?")
 parser$add_argument("--pheno-bool-remove-NA",                            dest="pheno_bool_remove_NA",                            type="logical", default=FALSE,                                                                     help="Remove samples missing phenotype data in the phenotype file? [default=FALSE].")
 parser$add_argument("--bool-within",                                     dest="bool_within",                                     type="logical", default=TRUE,                                                                      help="Perform within population k-fold cross-validation? [default=TRUE].")
 parser$add_argument("--bool-across",                                     dest="bool_across",                                     type="logical", default=FALSE,                                                                     help="Perform across populations cross-validations? [default=FALSE].")