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GO::TermFinderReport::Html.3pm
Langue: en
Version: 2007-03-18 (fedora - 01/12/10)
Section: 3 (Bibliothèques de fonctions)
NAME
GO::TermFinderReport::Html - prints an html table of the results of GO::TermFinderDESCRIPTION
This print() method of this Perl module receives a reference to an the array that is the return value from the findTerms method of GO::TermFinder, the aspect for which terms were found, the number of genes that were used to generate the terms, and the number of genes that were said to be in the genome. It will then generate an html table that summarizes those results. Optionally, filehandle, p-value cutoff, gene URL, and GOID URL arguments may also be passed in. Url links should have the string <REPLACE_THIS> to indicate where the gene name, or GOID should be put.SYNOPSIS
use GO::TermFinder; use GO::TermFinderReport::Html; . . . my @pvalues = $termFinder->findTerms(genes=>\@genes); my $report = GO::TermFinderReport::Html->new(); open (HTML, ">blah.html"); print HTML "<html><body>"; my $numRows = $report->print(pvalues => \@pvalues, aspect => $aspect, numGenes => scalar(@genes), totalNum => $totalNum, fh => \*HTML, cutoff => 0.01, geneUrl => 'http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>', goidUrl => 'http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=<REPLACE_THIS>'); print HTML "</body></html>"; close HTML;
new
This is the constructor.Usage:
my $report = GO::TermFinderReport::Html->new();
A GO::TermFinderReport::Html object is returned.
Usage:
my $numRows = $report->print(pvalues => \@pvalues, aspect => $aspect, # P, C, or F numGenes => scalar(@genes), totalNum => $totalNum, fh => \*HTML, pvalueCutOff => 0.01, geneUrl => 'http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>', goidUrl => 'http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=<REPLACE_THIS>');
Required arguments:
pvalues : A reference to the array returned by the findTerms() method of GO::TermFinder aspect : The aspect of the Gene Ontology for which terms were found (C, F or P) numGenes : The number of genes that were in the list passed to the findTerms method totalNum : The total number of genes that were indicated to be in the genome for finding terms.
Optional arguments:
fh : A reference to a file handle to which the table should be printed. Defaults to standard out. pvalueCutOff : The p-value cutoff, above which p-values and associated information will not be printed. Default is no cutoff. geneUrl : A url to which you want genes linked. Must contain the text '<REPLACE_THIS>', which will be replaced with the gene name. goidUrl : A url to which you want the GOIDs linked. Must contain the text '<REPLACE_THIS>', which will be replaced with the goid.
AUTHOR
Gavin Sherlocksherlock@genome.stanford.edu
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