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GO::TermFinderReport::Text.3pm
Langue: en
Version: 2007-03-23 (fedora - 01/12/10)
Section: 3 (Bibliothèques de fonctions)
NAME
GO::TermFinderReport::Text - prints results of GO::TermFinder as a text reportDESCRIPTION
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 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 a text report that summarizes those results. Optionally, filehandle and p-value cutoff arguments may also be passed in. It will return theSYNOPSIS
use GO::TermFinder; use GO::TermFinderReport::Text; . . . my @pvalues = $termFinder->findTerms(genes=>\@genes); my $report = GO::TermFinderReport::Text->new(); open (OUT, ">report.text"); my $numHypotheses = $report->print(pvalues => \@pvalues, aspect => $aspect, numGenes => scalar(@genes), totalNum => $totalNum, cutoff => 0.01, fh => \*OUT); close OUT;
new
This is the constructor.Usage:
my $report = GO::TermFinderReport::Text->new();
A GO::TermFinderReport::Text object is returned.
Usage:
my $numHypotheses = $report->print(pvalues => \@pvalues, numGenes => scalar(@genes), totalNum => $totalNum, cutoff => 0.01, fh => \*OUT, table => 0 );
Required arguments:
pvalues : A reference to the array returned by the findTerms() method
of GO::TermFinder
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.
cutoff : The p-value cutoff, above which p-values and associated
information will not be printed. Default is no cutoff.
table : 0 for standard output, 1 for tab delimited table. Default is 0
AUTHOR
Gavin Sherlocksherlock@genome.stanford.edu
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre