GO::TermFinderReport::User(Contributed Perl DocumGO::TermFinderReport::Html(3)NAMEGO::TermFinderReport::Html - prints an html table of the results of
GO::TermFinder
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 aspect for which terms were found, 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 an html
table that summarizes those results. Optionally, filehandle, p-value
cutoff, gene URL, and GOID URL arguments may also be passed in. Url
links should have the string <REPLACE_THIS> to indicate where the gene
name, or GOID should be put.
SYNOPSIS
use GO::TermFinder;
use GO::TermFinderReport::Html;
.
.
.
my @pvalues = $termFinder->findTerms(genes=>\@genes);
my $report = GO::TermFinderReport::Html->new();
open (HTML, ">blah.html");
print HTML "<html><body>";
my $numRows = $report->print(pvalues => \@pvalues,
aspect => $aspect,
numGenes => scalar(@genes),
totalNum => $totalNum,
fh => \*HTML,
cutoff => 0.01,
geneUrl => 'http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>',
goidUrl => 'http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=<REPLACE_THIS>');
print HTML "</body></html>";
close HTML;
new
This is the constructor.
Usage:
my $report = GO::TermFinderReport::Html->new();
A GO::TermFinderReport::Html object is returned.
print
This method prints out the report, in the form of an html table. The
table is ordered in ascending order of p-value (i.e. most significant
first), and will print out the GO node, the frequency of use of that
node within the selected group of genes, and the population as a whole,
the corrected p-value of that, and a list of the genes annotated to
that node. If the FDR was calculated, the FDR will also be printed.
It returns the number of annotation rows in the table that exceed the
provided p-value cutoff (which may even be zero, in which case nothing
is printed).
Usage:
my $numRows = $report->print(pvalues => \@pvalues,
aspect => $aspect, # P, C, or F
numGenes => scalar(@genes),
totalNum => $totalNum,
fh => \*HTML,
pvalueCutOff => 0.01,
geneUrl => 'http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>',
goidUrl => 'http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=<REPLACE_THIS>');
Required arguments:
pvalues : A reference to the array returned by the findTerms() method of GO::TermFinder
aspect : The aspect of the Gene Ontology for which terms were found (C, F or P)
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.
pvalueCutOff : The p-value cutoff, above which p-values and associated
information will not be printed. Default is no cutoff.
geneUrl : A url to which you want genes linked. Must contain the
text '<REPLACE_THIS>', which will be replaced with the
gene name.
goidUrl : A url to which you want the GOIDs linked. Must contain the
text '<REPLACE_THIS>', which will be replaced with the
goid.
AUTHOR
Gavin Sherlock
sherlock@genome.stanford.edu
perl v5.14.1 2007-03-18 GO::TermFinderReport::Html(3)
