--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_q_values.pl	Tue Apr 01 10:53:54 2014 -0400
@@ -0,0 +1,95 @@
+# A program to compute the q-values based on the p-values of multiple simultaneous tests. 
+# The q-valules are computed using a specific R package created by John Storey called "qvalue".
+# The input is a TABULAR format file consisting of one column only that represents the p-values 
+# of multiple simultaneous tests, one line for every p-value. 
+# The first output is a TABULAR format file consisting of one column only that represents the q-values 
+# corresponding to p-values, one line for every q-value. 
+# the second output is a TABULAR format file consisting of three pages: the first page represents 
+# the p-values histogram, the second page represents the q-values histogram, and the third page represents 
+# the four Q-plots as introduced in the "qvalue" package manual.
+
+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: compute_q_values.pl [TABULAR.in] [lambda] [pi0_method] [fdr_level] [robust] [TABULAR.out] [PDF.out] \n";
+die $usage unless @ARGV == 7;
+
+#get the input arguments
+my $p_valuesInputFile = $ARGV[0];
+my $lambdaValue =  $ARGV[1];
+my $pi0_method =  $ARGV[2];
+my $fdr_level =  $ARGV[3];
+my $robustValue =  $ARGV[4];
+my $q_valuesOutputFile = $ARGV[5];
+my $p_q_values_histograms_QPlotsFile = $ARGV[6];
+
+if($lambdaValue =~ /sequence/){
+	$lambdaValue = "seq(0, 0.95, 0.05)";
+}
+
+#open the input files
+open (INPUT, "<", $p_valuesInputFile) || die("Could not open file $p_valuesInputFile \n");
+open (OUTPUT1, ">", $q_valuesOutputFile) || die("Could not open file $q_valuesOutputFile \n");
+open (OUTPUT2, ">", $p_q_values_histograms_QPlotsFile) || die("Could not open file $p_q_values_histograms_QPlotsFile \n");
+#open (ERROR,  ">", "error.txt")  or die ("Could not open file error.txt \n");
+
+#save all error messages into the error file $errorFile using the error file handle ERROR
+#STDERR -> fdopen( \*ERROR,  "w" ) or die ("Could not direct errors to the error file error.txt \n");
+
+#warn "Hello Error File \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 = "q_values_computation.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; 
+print Rcmd "
+	#options(show.error.messages = FALSE);
+	
+	#load necessary packages
+	suppressPackageStartupMessages(library(tcltk));
+	library(qvalue);
+	
+	#read the p-values of the multiple simultaneous tests from the input file $p_valuesInputFile
+	p <- scan(\"$p_valuesInputFile\", quiet = TRUE);
+	
+	#compute the q-values that correspond to the p-values of the multiple simultaneous tests
+	qobj <- qvalue(p, pi0.meth = \"$pi0_method\", lambda = $lambdaValue, fdr.level = $fdr_level, robust = $robustValue);
+	#qobj <- qvalue(p, pi0.meth = \"smoother\", lambda = seq(0, 0.95, 0.05), fdr.level = 0.05);
+	#qobj <- qvalue(p, pi0.meth = \"bootstrap\", fdr.level = 0.05);
+	
+	#draw the p-values histogram, the q-values histogram, and the four Q-plots 
+	# and save them on multiple pages of the output file $p_q_values_histograms_QPlotsFile
+	pdf(file = \"$p_q_values_histograms_QPlotsFile\", width = 6.25, height = 6, family = \"Times\", pointsize = 12, onefile = TRUE)
+	hist(qobj\$pvalues);
+	#dev.off();
+	
+	hist(qobj\$qvalues);
+	#dev.off(); 
+	
+	qplot(qobj);  
+	dev.off();
+	
+	#save the q-values in the output file $q_valuesOutputFile
+	qobj\$pi0 <- signif(qobj\$pi0,digits=6)
+	qwrite(qobj, filename=\"$q_valuesOutputFile\"); 
+
+	#options(show.error.messages = TRUE);
+	#eof\n";
+close Rcmd;	
+
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+
+#close the input and output and error files
+#close(ERROR);
+close(OUTPUT2);
+close(OUTPUT1);
+close(INPUT);