use a smaller file to actually run SKAT

akotlar · Aug 29, 2018 · 66c8414 · 66c8414
1 parent 6c71950
commit 66c8414
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/bin/SKAT_template.R b/bin/SKAT_template.R
@@ -72,14 +72,14 @@ if(!is.null(file.cov)) {
   yCov <- famCov$Phenotype
   sex <- famCov$Sex
 
-  obj<-SKAT_Null_Model(yCov ~ x1 + x2 + x3 + x4 + sex, out_type="D", n.Resampling=1000, type.Resampling='bootstrap') 
+  obj<-SKAT_Null_Model(yCov ~ x1 + x2 + x3 + x4 + sex, out_type="D") #n.Resampling=1000, type.Resampling='bootstrap'
 } else {
   famCov <- Read_Plink_FAM(file.fam, Is.binary=TRUE)
 
   yCov <- famCov$Phenotype
   sex <- famCov$Sex
 
-  obj<-SKAT_Null_Model(yCov ~ sex, out_type="D", n.Resampling=1000, type.Resampling='bootstrap') 
+  obj<-SKAT_Null_Model(yCov ~ sex, out_type="D") #n.Resampling=1000, type.Resampling='bootstrap'
 }
 
 

diff --git a/bin/run_skat_example.sh b/bin/run_skat_example.sh
@@ -12,7 +12,7 @@ mkdir -p ./log;
 # * needed instead of ./ to prevent ./filename.annotaiton.tsv.gz
 annotation=1000g_100klines_example_old.annotation.tsv.gz;
 annotationBaseName=1000g_100klines_example.annotation;
-annotationVcfGz=1000g_100klines_old_example.annotation.vcf.gz;
+annotationVcfGz=1000g_100klines_old_example.annotation.20klines.vcf.gz;
 annotationSampleList=1000g_100klines_example.annotation.sample_list;
 
 fam=1000g_100klines_example.fake.fam

diff --git a/example/1000g_100klines_old_example.annotation.20klines.vcf.gz b/example/1000g_100klines_old_example.annotation.20klines.vcf.gz