1GO::TermFinderReport::TUesxetr(3C)ontributed Perl DocumeGnOt:a:tTieornmFinderReport::Text(3)
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NAME

6       GO::TermFinderReport::Text - prints results of GO::TermFinder as a text
7       report
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DESCRIPTION

10       This print() method of this Perl module receives a reference to an the
11       array that is the return value from the findTerms method of
12       GO::TermFinder, the number of genes that were used to generate the
13       terms, and the number of genes that were said to be in the genome.  It
14       will then generate a text report that summarizes those results.
15       Optionally, filehandle and p-value cutoff arguments may also be passed
16       in.  It will return the
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SYNOPSIS

19           use GO::TermFinder;
20           use GO::TermFinderReport::Text;
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22           .
23           .
24           .
25
26           my @pvalues = $termFinder->findTerms(genes=>\@genes);
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28           my $report  = GO::TermFinderReport::Text->new();
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30           open (OUT, ">report.text");
31
32           my $numHypotheses = $report->print(pvalues  => \@pvalues,
33                                              aspect   => $aspect,
34                                              numGenes => scalar(@genes),
35                                              totalNum => $totalNum,
36                                              cutoff   => 0.01,
37                                              fh       => \*OUT);
38
39           close OUT;
40
41   new
42       This is the constructor.
43
44       Usage:
45
46           my $report = GO::TermFinderReport::Text->new();
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48       A GO::TermFinderReport::Text object is returned.
49
50   print
51       This method prints out the text report of the passed in hypotheses.
52       The report is ordered in ascending order of p-value (i.e. most
53       significant first).  If the FDR was calculated, the FDR will also be
54       printed.  It returns the number of hypotheses that had corrected
55       p-values as good or better than the passed in cutoff.
56
57       Usage:
58
59           my $numHypotheses = $report->print(pvalues  => \@pvalues,
60                                              numGenes => scalar(@genes),
61                                              totalNum => $totalNum,
62                                              cutoff   => 0.01,
63                                              fh       => \*OUT,
64                                              table    => 0 );
65
66       Required arguments:
67
68       pvalues  : A reference to the array returned by the findTerms() method
69                  of GO::TermFinder
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71       numGenes : The number of genes that were in the list passed to the
72                  findTerms method
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74       totalNum : The total number of genes that were indicated to be in the
75                  genome for finding terms.
76
77       Optional arguments:
78
79       fh       : A reference to a file handle to which the table should be
80                  printed.  Defaults to standard out.
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82       cutoff   : The p-value cutoff, above which p-values and associated
83                  information will not be printed.  Default is no cutoff.
84
85       table    : 0 for standard output, 1 for tab delimited table.  Default
86       is 0
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AUTHOR

89       Gavin Sherlock
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91       sherlock@genome.stanford.edu
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95perl v5.28.0                      2007-03-23     GO::TermFinderReport::Text(3)