1GO::TermFinderReport::HUtsmelr(3C)ontributed Perl DocumeGnOt:a:tTieornmFinderReport::Html(3)
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NAME

6       GO::TermFinderReport::Html - prints an html table of the results of
7       GO::TermFinder
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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 aspect for which terms were found, the number of
13       genes that were used to generate the terms, and the number of genes
14       that were said to be in the genome.  It will then generate an html
15       table that summarizes those results.  Optionally, filehandle, p-value
16       cutoff, gene URL, and GOID URL arguments may also be passed in.  Url
17       links should have the string <REPLACE_THIS> to indicate where the gene
18       name, or GOID should be put.
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SYNOPSIS

21           use GO::TermFinder;
22           use GO::TermFinderReport::Html;
23
24           .
25           .
26           .
27
28           my @pvalues = $termFinder->findTerms(genes=>\@genes);
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30           my $report  = GO::TermFinderReport::Html->new();
31
32           open (HTML, ">blah.html");
33
34           print HTML "<html><body>";
35
36           my $numRows = $report->print(pvalues  => \@pvalues,
37                                        aspect   => $aspect,
38                                        numGenes => scalar(@genes),
39                                        totalNum => $totalNum,
40                                        fh       => \*HTML,
41                                        cutoff   => 0.01,
42                                        geneUrl  => 'http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>',
43                                        goidUrl  => 'http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=<REPLACE_THIS>');
44
45           print HTML "</body></html>";
46
47           close HTML;
48
49   new
50       This is the constructor.
51
52       Usage:
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54           my $report = GO::TermFinderReport::Html->new();
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56       A GO::TermFinderReport::Html object is returned.
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58   print
59       This method prints out the report, in the form of an html table.  The
60       table is ordered in ascending order of p-value (i.e. most significant
61       first), and will print out the GO node, the frequency of use of that
62       node within the selected group of genes, and the population as a whole,
63       the corrected p-value of that, and a list of the genes annotated to
64       that node.  If the FDR was calculated, the FDR will also be printed.
65       It returns the number of annotation rows in the table that exceed the
66       provided p-value cutoff (which may even be zero, in which case nothing
67       is printed).
68
69       Usage:
70
71           my $numRows = $report->print(pvalues      => \@pvalues,
72                                        aspect       => $aspect,   # P, C, or F
73                                        numGenes     => scalar(@genes),
74                                        totalNum     => $totalNum,
75                                        fh           => \*HTML,
76                                        pvalueCutOff => 0.01,
77                                        geneUrl      => 'http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>',
78                                        goidUrl      => 'http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=<REPLACE_THIS>');
79
80       Required arguments:
81
82           pvalues   :  A reference to the array returned by the findTerms() method of GO::TermFinder
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84           aspect    :  The aspect of the Gene Ontology for which terms were found (C, F or P)
85
86           numGenes  :  The number of genes that were in the list passed to the findTerms method
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88           totalNum  :  The total number of genes that were indicated to be in the genome for finding terms.
89
90       Optional arguments:
91
92           fh       : A reference to a file handle to which the table should be
93                      printed.  Defaults to standard out.
94
95           pvalueCutOff   : The p-value cutoff, above which p-values and associated
96                            information will not be printed.  Default is no cutoff.
97
98           geneUrl  : A url to which you want genes linked.  Must contain the
99                      text '<REPLACE_THIS>', which will be replaced with the
100                      gene name.
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102           goidUrl  : A url to which you want the GOIDs linked.  Must contain the
103                      text '<REPLACE_THIS>', which will be replaced with the
104                      goid.
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AUTHOR

107       Gavin Sherlock
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109       sherlock@genome.stanford.edu
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113perl v5.28.0                      2007-03-18     GO::TermFinderReport::Html(3)
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