GO::TermFinderReport::User(Contributed Perl DocumGO::TermFinderReport::Text(3)NAMEGO::TermFinderReport::Text - prints results of GO::TermFinder as a text
report
DESCRIPTION
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 the
SYNOPSIS
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.
print
This method prints out the text report of the passed in hypotheses.
The report is ordered in ascending order of p-value (i.e. most
significant first). If the FDR was calculated, the FDR will also be
printed. It returns the number of hypotheses that had corrected
p-values as good or better than the passed in cutoff.
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 Sherlock
sherlock@genome.stanford.edu
perl v5.14.1 2007-03-23 GO::TermFinderReport::Text(3)
