GO::TermFinderReport::Text - prints results of GO::TermFinder as a text report

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

    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;

This is the constructor.

Usage:

    my $report = GO::TermFinderReport::Text->new();

A GO::TermFinderReport::Text object is returned.

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

Gavin Sherlock

sherlock@genome.stanford.edu