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.
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.
my $numHypotheses = $report->print(pvalues => \@pvalues, numGenes => scalar(@genes), totalNum => $totalNum, cutoff => 0.01, fh => \*OUT, table => 0 );
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.
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