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author | devteam |
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date | Tue, 13 Oct 2015 12:32:54 -0400 |
parents | 3d24b35de20a |
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# A program to implement the non-pooled t-test for two samples where the alternative hypothesis is two-sided or one-sided. # The first input file is a TABULAR format file representing the first sample and consisting of one column only. # The second input file is a TABULAR format file representing the first sample nd consisting of one column only. # The third input is the sidedness of the t-test: either two-sided or, one-sided with m1 less than m2 or, # one-sided with m1 greater than m2. # The fourth input is the equality status of the standard deviations of both populations # The output file is a TXT file representing the result of the two sample t-test. use strict; use warnings; #variable to handle the motif information my $motif; my $motifName = ""; my $motifNumber = 0; my $totalMotifsNumber = 0; my @motifNamesArray = (); # check to make sure having correct files my $usage = "usage: non_pooled_t_test_two_samples_galaxy.pl [TABULAR.in] [TABULAR.in] [testSidedness] [standardDeviationEquality] [TXT.out] \n"; die $usage unless @ARGV == 5; #get the input arguments my $firstSampleInputFile = $ARGV[0]; my $secondSampleInputFile = $ARGV[1]; my $testSidedness = $ARGV[2]; my $standardDeviationEquality = $ARGV[3]; my $outputFile = $ARGV[4]; #open the input files open (INPUT1, "<", $firstSampleInputFile) || die("Could not open file $firstSampleInputFile \n"); open (INPUT2, "<", $secondSampleInputFile) || die("Could not open file $secondSampleInputFile \n"); open (OUTPUT, ">", $outputFile) || die("Could not open file $outputFile \n"); #variables to store the name of the R script file my $r_script; # R script to implement the two-sample test on the motif frequencies in upstream flanking region #construct an R script file and save it in the same directory where the perl file is located $r_script = "non_pooled_t_test_two_samples.r"; open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; print Rcmd " sampleTable1 <- read.table(\"$firstSampleInputFile\", header=FALSE); sample1 <- sampleTable1[, 1]; sampleTable2 <- read.table(\"$secondSampleInputFile\", header=FALSE); sample2 <- sampleTable2[, 1]; testSideStatus <- \"$testSidedness\"; STEqualityStatus <- \"$standardDeviationEquality\"; #open the output a text file sink(file = \"$outputFile\"); #check if the t-test is two-sided if (testSideStatus == \"two-sided\"){ #check if the standard deviations are equal in both populations if (STEqualityStatus == \"equal\"){ #two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided testResult <- t.test(sample1, sample2, var.equal = TRUE); } else{ #two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided testResult <- t.test(sample1, sample2, var.equal = FALSE); } } else{ #the t-test is one sided #check if the t-test is two-sided with m1 < m2 if (testSideStatus == \"one-sided:_m1_less_than_m2\"){ #check if the standard deviations are equal in both populations if (STEqualityStatus == \"equal\"){ #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2 testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"less\"); } else{ #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2 testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"less\"); } } else{ #the t-test is one-sided with m1 > m2 #check if the standard deviations are equal in both populations if (STEqualityStatus == \"equal\"){ #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2 testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"greater\"); } else{ #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2 testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"greater\"); } } } #save the output of the t-test into the output text file testResult; #close the output text file sink(); #eof" . "\n"; close Rcmd; system("R --no-restore --no-save --no-readline < $r_script > $r_script.out"); #close the input and output files close(OUTPUT); close(INPUT2); close(INPUT1);