Merge pull request #22 from FredHutch/v1.2-patch-191104

Update SEACR_1.2.sh
FredHutch · Nov 5, 2019 · 46fb539 · 46fb539
2 parents 8ed4b16 + 169c97f
commit 46fb539
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diff --git a/SEACR_1.2.R b/SEACR_1.2.R
@@ -137,6 +137,7 @@ if(is.na(numtest)){ ## If 2nd field is a bedgraph, calculate empirical threshold
 	ctrl<-as.vector(as.numeric(paste(0,argsL$ctrl,sep="")))
 	x0<-min(frame$values[frame$percentile <= ctrl[1]])
 	z0<-min(frame2$values[frame2$percentile <= ctrl[1]])
+	d0<-0
 	fdr<-ctrl[1] ## New for SEACR_1.1
 }
 invis <- gc(verbose=FALSE)

diff --git a/SEACR_1.2.sh b/SEACR_1.2.sh
@@ -119,14 +119,14 @@ path=`dirname $0`
 if [[ -f $2 ]] && [[ $norm == "norm" ]]
 then
 	echo "Calculating threshold using normalized control: $(date)"
-	Rscript $path/SEACR_1.1.R --exp=$password.auc --ctrl=$password2.auc --norm=yes --output=$password
+	Rscript $path/SEACR_1.2.R --exp=$password.auc --ctrl=$password2.auc --norm=yes --output=$password
 elif [[ -f $2 ]]
 then
 	echo "Calculating threshold using non-normalized control: $(date)"
-	Rscript $path/SEACR_1.1.R --exp=$password.auc --ctrl=$password2.auc --norm=no --output=$password
+	Rscript $path/SEACR_1.2.R --exp=$password.auc --ctrl=$password2.auc --norm=no --output=$password
 else
 	echo "Using user-provided threshold: $(date)"
-	Rscript $path/SEACR_1.1.R --exp=$password.auc --ctrl=$2 --norm=no --output=$password
+	Rscript $path/SEACR_1.2.R --exp=$password.auc --ctrl=$2 --norm=no --output=$password
 fi
 
 fdr=`cat $password.fdr.txt | sed -n '1p'`			## Added 5/15/19 for SEACR_1.1