--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/calculateZPrimeFactor.pl	Wed Jun 01 03:37:27 2016 -0400
@@ -0,0 +1,102 @@
+###############################################################################
+# In summary this script calculates the z prime factor for one or more plates
+# of data.
+#
+# Args:
+#   input.data.frame contains one or more columns of plate data. The first column 
+#   must contain the well annotation ie A01, A02 etc. Each subsequent column represents
+#   a plate of data where the column name is the plate name.
+#
+#   plate.conf.data.frame is a file of the following format:
+#	  well, type(syntax must be either "poscontr" or "negcontr"), name (name of control)
+#
+# Returns:
+#    z'factor for each plate for each combination of each type of positive vs negative control.
+#
+# Author: gouldkate
+###############################################################################
+
+use strict;
+use warnings;
+use IO::Handle;
+use File::Temp qw/ tempfile tempdir /;
+my $tdir = tempdir( CLEANUP => 0 );
+
+# check to make sure having correct input and output files
+my $usage = "usage: calculateZPrimeFactor.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n";
+die $usage unless @ARGV == 3;
+
+#get the input arguments
+my $plateData = $ARGV[0];
+my $plateConfig =  $ARGV[1];
+my $zPrimeFactor =  $ARGV[2];
+
+#open the input files
+open (INPUT1, "<", $plateData) || die("Could not open file $plateData \n");
+open (INPUT2, "<", $plateConfig) || die("Could not open file $plateConfig \n");
+open (OUTPUT1, ">", $zPrimeFactor) || die("Could not open file $zPrimeFactor \n");
+
+#variable to store the name of the R script file
+my $r_script;
+
+# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values 	
+# construct an R script file and save it in a temp directory
+chdir $tdir;
+$r_script = "calculateZPrimeFactor.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; 
+print Rcmd "
+	#options(show.error.messages = FALSE);
+	input.data.frame <- read.table(\"$plateData\", head=T, sep=\"\\t\", comment=\"\");
+	plate.conf.data.frame <- read.table(\"$plateConfig\", head=T, sep=\"\\t\", comment=\"\");
+	
+	# assumed second column is type ie negcontr or poscontr and third column is name of control
+	negative.controls.list <- unique(plate.conf.data.frame[which (plate.conf.data.frame[,2] == \"negcontr\"),][,3])
+	positive.controls.list <- unique(plate.conf.data.frame[which (plate.conf.data.frame[,2] == \"poscontr\"),][,3])
+  
+	z.prime.factor.report.data.frame <- data.frame()
+  
+  
+	for (negative.control in negative.controls.list){
+		for (positive.control in positive.controls.list){
+			for (i in 2:length(colnames(input.data.frame))){
+        
+				negative.control.wells <- plate.conf.data.frame[which (plate.conf.data.frame[3] == negative.control),][,1]
+				positive.control.wells <- plate.conf.data.frame[which (plate.conf.data.frame[3] == positive.control),][,1]
+
+				control.duo <- paste(negative.control, positive.control, sep=\"/\")
+				
+				negative.control.values <- input.data.frame[((input.data.frame[,1] %in% negative.control.wells)&(!(is.na(input.data.frame[,i])))),][,i]
+				positive.control.values <- input.data.frame[((input.data.frame[,1] %in% positive.control.wells)&(!(is.na(input.data.frame[,i])))),][,i]
+
+				if ((length(negative.control.values)==0)|(length(positive.control.values)==0)){
+					z.prime.factor <- NA
+				} else {
+					if ((sum(negative.control.values)) < (sum(positive.control.values))){
+						low.value.controls <- negative.control.values
+						high.value.controls <- positive.control.values
+					} else {
+						low.value.controls <- positive.control.values
+						high.value.controls <- negative.control.values
+					}
+					z.prime.factor <- round(1 - ((3 * (sd(high.value.controls, na.rm = TRUE) + sd(low.value.controls, na.rm = TRUE))/(abs(mean(high.value.controls, na.rm = TRUE) - mean(low.value.controls, na.rm = TRUE))))), 2)
+				}
+				
+				plate.name <- colnames(input.data.frame)[i]
+				z.prime.factor.current.row.data.frame <- data.frame(plate=plate.name, control.duo=control.duo, z.prime.factor=z.prime.factor, stringsAsFactors=FALSE)
+				z.prime.factor.report.data.frame <-rbind(z.prime.factor.report.data.frame, z.prime.factor.current.row.data.frame)
+			}
+		}
+	}
+	z.prime.factor.report.data.frame <- z.prime.factor.report.data.frame[order(z.prime.factor.report.data.frame\$control.duo),]
+	write.table(z.prime.factor.report.data.frame, file=\"$zPrimeFactor\", quote=F, sep=\"\\t\", row.names=F);
+	#eof\n";
+
+close Rcmd;	
+
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+
+#close the input and output files
+close(OUTPUT1);
+close(INPUT1);
+close(INPUT2);