GOstats and htmlReport

0

Entering edit mode

Loren Engrav ★ 1.0k

@loren-engrav-2040

Last seen 10.2 years ago

Hi Have GOstats up and see > GOstatsSummary01 <- summary(GOstatsOver01, htmlLinks="true") > class(GOstatsSummary01) [1] "data.frame" > htmlReport(GOstatsSummary01, file="GOstatsSummary01.html") Error in function (classes, fdef, mtable) : unable to find an inherited method for function "htmlReport", for signature "data.frame" What am I missing please? Thank you ================= > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] SparseM_0.85 RBGL_1.24.0 Rgraphviz_1.26.0 xtable_1.5-6 RColorBrewer_1.0-2 GOstats_2.14.0 graph_1.26.0 Category_2.14.0 [9] genefilter_1.30.0 annotate_1.26.0 GO.db_2.4.1 hgu133plus2.db_2.4.1 org.Hs.eg.db_2.4.1 RSQLite_0.8-4 DBI_0.2-5 AnnotationDbi_1.10.0 [17] ALL_1.4.7 Biobase_2.8.0 loaded via a namespace (and not attached): [1] GSEABase_1.10.0 splines_2.11.0 survival_2.35-8 tools_2.11.0 XML_2.8-1

GO GOstats GO GOstats • 1.5k views

ADD COMMENT • link updated 14.6 years ago by Seth Falcon ★ 7.4k • written 14.6 years ago by Loren Engrav ★ 1.0k

0

Entering edit mode

Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 10.2 years ago

Hi Loren, On 4/25/10 6:13 PM, Loren Engrav wrote: > Have GOstats up and see > >> GOstatsSummary01 <- summary(GOstatsOver01, htmlLinks="true") > >> class(GOstatsSummary01) > [1] "data.frame" > >> htmlReport(GOstatsSummary01, file="GOstatsSummary01.html") > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "htmlReport", for > signature "data.frame" > > What am I missing please? The documentation? :-) htmlReport is expecting a HyperGResult object. So I think you should be able to call: htmlReport(GOstatsOver01). I can see how you may have been misled by the docs, which say: > htmlReport writes an HTML version of the table produced by the > ?summary? method. But the next sentence is: > The first argument should be a > ?HyperGResult? instance (or subclass). + seth

ADD COMMENT • link 14.6 years ago Seth Falcon ★ 7.4k

0

Entering edit mode

Thank you Solved > From: Seth Falcon <sfalcon at="" fhcrc.org=""> > Date: Sun, 25 Apr 2010 21:01:20 -0700 > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] GOstats and htmlReport > > Hi Loren, > > On 4/25/10 6:13 PM, Loren Engrav wrote: >> Have GOstats up and see >> >>> GOstatsSummary01 <- summary(GOstatsOver01, htmlLinks="true") >> >>> class(GOstatsSummary01) >> [1] "data.frame" >> >>> htmlReport(GOstatsSummary01, file="GOstatsSummary01.html") >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "htmlReport", for >> signature "data.frame" >> >> What am I missing please? > > The documentation? :-) > > htmlReport is expecting a HyperGResult object. So I think you should be > able to call: > > htmlReport(GOstatsOver01). > > I can see how you may have been misled by the docs, which say: > >> htmlReport writes an HTML version of the table produced by the >> ?summary? method. > > But the next sentence is: > >> The first argument should be a >> ?HyperGResult? instance (or subclass). > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 14.6 years ago Loren Engrav ★ 1.0k

Login before adding your answer.