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GO::TermFinderReport::Text.3pm

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