.\" Automatically generated by Pod::Man 4.11 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "GO::TermFinderReport::Html 3" .TH GO::TermFinderReport::Html 3 "2007-03-18" "perl v5.28.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" GO::TermFinderReport::Html \- prints an html table of the results of GO::TermFinder .SH "DESCRIPTION" .IX Header "DESCRIPTION" This \fBprint()\fR 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 \s-1URL,\s0 and \s-1GOID URL\s0 arguments may also be passed in. Url links should have the string <\s-1REPLACE_THIS\s0> to indicate where the gene name, or \s-1GOID\s0 should be put. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& use GO::TermFinder; \& use GO::TermFinderReport::Html; \& \& . \& . \& . \& \& my @pvalues = $termFinder\->findTerms(genes=>\e@genes); \& \& my $report = GO::TermFinderReport::Html\->new(); \& \& open (HTML, ">blah.html"); \& \& print HTML ""; \& \& my $numRows = $report\->print(pvalues => \e@pvalues, \& aspect => $aspect, \& numGenes => scalar(@genes), \& totalNum => $totalNum, \& fh => \e*HTML, \& cutoff => 0.01, \& geneUrl => \*(Aqhttp://db.yeastgenome.org/cgi\-bin/SGD/locus.pl?locus=\*(Aq, \& goidUrl => \*(Aqhttp://amigo.geneontology.org/cgi\-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=\*(Aq); \& \& print HTML ""; \& \& close HTML; .Ve .SS "new" .IX Subsection "new" This is the constructor. .PP Usage: .PP .Vb 1 \& my $report = GO::TermFinderReport::Html\->new(); .Ve .PP A GO::TermFinderReport::Html object is returned. .SS "print" .IX Subsection "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 \s-1GO\s0 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 \s-1FDR\s0 was calculated, the \s-1FDR\s0 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). .PP Usage: .PP .Vb 8 \& my $numRows = $report\->print(pvalues => \e@pvalues, \& aspect => $aspect, # P, C, or F \& numGenes => scalar(@genes), \& totalNum => $totalNum, \& fh => \e*HTML, \& pvalueCutOff => 0.01, \& geneUrl => \*(Aqhttp://db.yeastgenome.org/cgi\-bin/SGD/locus.pl?locus=\*(Aq, \& goidUrl => \*(Aqhttp://amigo.geneontology.org/cgi\-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=\*(Aq); .Ve .PP Required arguments: .PP .Vb 1 \& 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. .Ve .PP Optional arguments: .PP .Vb 2 \& 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 \*(Aq\*(Aq, which will be replaced with the \& gene name. \& \& goidUrl : A url to which you want the GOIDs linked. Must contain the \& text \*(Aq\*(Aq, which will be replaced with the \& goid. .Ve .SH "AUTHOR" .IX Header "AUTHOR" Gavin Sherlock .PP sherlock@genome.stanford.edu