/ 
GO-TermFinder-0.86
River stage zero No dependents
/ GO::TermFinderReport::Text

NAME

GO::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