--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalizeMedianNegCntrl.pl	Wed Jun 01 03:52:52 2016 -0400
@@ -0,0 +1,87 @@
+###############################################################################
+# In summary this script normalizes each plate of input data to each of its negative
+# controls.
+#
+# 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" or "empty"), name (name of control)
+#
+# Returns:
+#   plate values normalized to each negative control type per plate.
+#
+# Author: kate gould
+###############################################################################
+
+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: normalizeMedianNegCntrl.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 $normMedNeg =  $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, ">", $normMedNeg) || die("Could not open file $normMedNeg \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 = "normalizeMedianNegCntrl.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; 
+print Rcmd "
+	#options(show.error.messages = FALSE);
+	header <- read.table(\"$plateData\", head=F, sep=\"\\t\", comment=\"\", nrows=1);
+	input.data.frame <- read.table(\"$plateData\", head=F, sep=\"\\t\", skip=1);
+	plate.conf.data.frame <- read.table(\"$plateConfig\", head=T, sep=\"\\t\", comment=\"\");
+
+	normalise <- function(x, y){if (!is.na(x)) return (x/y) else (return (NA))}
+	
+	# assumed second column is type ie negcontr and third column is name of control
+	negative.controls.list <- unique(plate.conf.data.frame[which (plate.conf.data.frame[,2] == \"negcontr\"),][,3]);
+	
+	normalized.data.frame <- data.frame(well=input.data.frame[,1], stringsAsFactors=FALSE);
+	column.name.list <- c();
+	for (negative.control in negative.controls.list){
+		negative.control.wells <- plate.conf.data.frame[which (plate.conf.data.frame[3] == negative.control),][,1];
+		
+		for (i in 2:length(colnames(input.data.frame))){
+			column.name <- paste(colnames(input.data.frame)[i], \".normalised.to.\", negative.control, sep=\"\");
+			column.name.list <- append(column.name.list, column.name);
+			
+			negative.control.values <- input.data.frame[((input.data.frame[,1] %in% negative.control.wells)&(!(is.na(input.data.frame[,i])))),][,i];
+			median.negative.value <- median(negative.control.values);
+			
+			normalised.to.median.negative.control.value <- round(sapply(input.data.frame[,i], FUN=normalise, median.negative.value), 2);
+			normalized.data.frame <- cbind(normalized.data.frame, normalised.to.median.negative.control.value);
+		}
+	}  
+	header <- c(header[1], column.name.list)
+	write.table(header, file=\"$normMedNeg\", quote=F, sep=\"\\t\", row.names=F, col.names=F);
+	write.table(normalized.data.frame, file=\"$normMedNeg\", quote=F, sep=\"\\t\", row.names=F, col.names=F, append=T);
+	#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);