Mercurial > repos > xuebing > sharplabtool

comparison tools/regVariation/t_test_two_samples.pl @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 # A program to implement the non-pooled t-test for two samples where the alternative hypothesis is two-sided or one-sided.
2 # The first input file is a TABULAR format file representing the first sample and consisting of one column only.
3 # The second input file is a TABULAR format file representing the first sample nd consisting of one column only.
4 # The third input is the sidedness of the t-test: either two-sided or, one-sided with m1 less than m2 or,
5 # one-sided with m1 greater than m2.
6 # The fourth input is the equality status of the standard deviations of both populations
7 # The output file is a TXT file representing the result of the two sample t-test.
8
9 use strict;
10 use warnings;
11
12 #variable to handle the motif information
13 my $motif;
14 my $motifName = "";
15 my $motifNumber = 0;
16 my $totalMotifsNumber = 0;
17 my @motifNamesArray = ();
18
19 # check to make sure having correct files
20 my $usage = "usage: non_pooled_t_test_two_samples_galaxy.pl [TABULAR.in] [TABULAR.in] [testSidedness] [standardDeviationEquality] [TXT.out] \n";
21 die $usage unless @ARGV == 5;
22
23 #get the input arguments
24 my $firstSampleInputFile = $ARGV[0];
25 my $secondSampleInputFile = $ARGV[1];
26 my $testSidedness = $ARGV[2];
27 my $standardDeviationEquality = $ARGV[3];
28 my $outputFile = $ARGV[4];
29
30 #open the input files
31 open (INPUT1, "<", $firstSampleInputFile) || die("Could not open file $firstSampleInputFile \n");
32 open (INPUT2, "<", $secondSampleInputFile) || die("Could not open file $secondSampleInputFile \n");
33 open (OUTPUT, ">", $outputFile) || die("Could not open file $outputFile \n");
34
35
36 #variables to store the name of the R script file
37 my $r_script;
38
39 # R script to implement the two-sample test on the motif frequencies in upstream flanking region
40 #construct an R script file and save it in the same directory where the perl file is located
41 $r_script = "non_pooled_t_test_two_samples.r";
42
43 open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
44 print Rcmd "
45 sampleTable1 <- read.table(\"$firstSampleInputFile\", header=FALSE);
46 sample1 <- sampleTable1[, 1];
47
48 sampleTable2 <- read.table(\"$secondSampleInputFile\", header=FALSE);
49 sample2 <- sampleTable2[, 1];
50
51 testSideStatus <- \"$testSidedness\";
52 STEqualityStatus <- \"$standardDeviationEquality\";
53
54 #open the output a text file
55 sink(file = \"$outputFile\");
56
57 #check if the t-test is two-sided
58 if (testSideStatus == \"two-sided\"){
59
60 #check if the standard deviations are equal in both populations
61 if (STEqualityStatus == \"equal\"){
62 #two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided
63 testResult <- t.test(sample1, sample2, var.equal = TRUE);
64 } else{
65 #two-sample t-test where standard deviations are assumed to be unequal, the test is two-sided
66 testResult <- t.test(sample1, sample2, var.equal = FALSE);
67 }
68 } else{ #the t-test is one sided
69
70 #check if the t-test is two-sided with m1 < m2
71 if (testSideStatus == \"one-sided:_m1_less_than_m2\"){
72
73 #check if the standard deviations are equal in both populations
74 if (STEqualityStatus == \"equal\"){
75 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
76 testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"less\");
77 } else{
78 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
79 testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"less\");
80 }
81 } else{ #the t-test is one-sided with m1 > m2
82 #check if the standard deviations are equal in both populations
83 if (STEqualityStatus == \"equal\"){
84 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
85 testResult <- t.test(sample1, sample2, var.equal = TRUE, alternative = \"greater\");
86 } else{
87 #two-sample t-test where standard deviations are assumed to be unequal, the test is one-sided: Halt: m1 < m2
88 testResult <- t.test(sample1, sample2, var.equal = FALSE, alternative = \"greater\");
89 }
90 }
91 }
92
93 #save the output of the t-test into the output text file
94 testResult;
95
96 #close the output text file
97 sink();
98
99 #eof" . "\n";
100
101 close Rcmd;
102
103 system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
104
105 #close the input and output files
106 close(OUTPUT);
107 close(INPUT2);
108 close(INPUT1);
109