KEGG & hyperGTest: an example?

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Paul Shannon ★ 1.1k

@paul-shannon-578

Last seen 10.2 years ago

Can anyone direct me to an example of using hyperGTest with a KEGGHyperGParams? My organism is yeast and -- since my experimental data is from proteomics -- I have been happy using the YEAST annotation package, rather than annotation for a particular chip: params = new ("GOHyperGParams", geneIds = unique (genes), universeGeneIds = character (0), annotation = "YEAST", ontology = ontology, pvalueCutoff = pvalue, conditional = FALSE, testDirection = "over") hgr = hyperGTest (params) I'd be delighted to find a similar example for yeast & KEGG. My own experiments and web searching didn't get me far. Thanks! - Paul

Annotation Yeast Organism Annotation Yeast Organism • 1.8k views

ADD COMMENT • link updated 17.1 years ago by Seth Falcon ▴ 150 • written 17.1 years ago by Paul Shannon ★ 1.1k

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Seth Falcon ▴ 150

@seth-falcon-2443

Last seen 10.2 years ago

Paul Shannon <pshannon at="" systemsbiology.org=""> writes: > Can anyone direct me to an example of using hyperGTest with a > KEGGHyperGParams? > > My organism is yeast and -- since my experimental data is from > proteomics -- I > have been happy using the YEAST annotation package, rather than > annotation > for a particular chip: > > params = new ("GOHyperGParams", geneIds = unique (genes), > universeGeneIds = character (0), annotation = "YEAST", > ontology = ontology, pvalueCutoff = pvalue, > conditional = FALSE, > testDirection = "over") > > hgr = hyperGTest (params) > > I'd be delighted to find a similar example for yeast & KEGG. My own > experiments > and web searching didn't get me far. Does this not work? > params = new("KEGGHyperGParams", geneIds = unique(genes), > universeGeneIds = character(0), annotation = "YEAST", > ontology = ontology, pvalueCutoff = pvalue, > conditional = FALSE, > testDirection = "over") (although I'm confused why specifying zero-length for universeGeneIds makes any sense...) + seth -- Seth Falcon | seth at userprimary.net | blog: http://userprimary.net/user/

ADD COMMENT • link 17.1 years ago Seth Falcon ▴ 150

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With Seth's prompting :} I went back and fiddled a while longer with my KEGGHyperGParams. I eventually found the right combination, which I include below (along with a PFAMHyperGParams example) in case it might be useful to someone. As for Seth's other comment: > (although I'm confused why specifying zero-length for universeGeneIds > makes any sense...) I think it does make sense as long as the goal of the analysis is annotation, rather than enrichment. The Category package is a very handy way to discover, for example, which GO terms, KEGG pathways, and PFAM domains are shared among proteins, as I try to elucidate the results of experiments in phosphoproteomics. ---- KEGG and YEAST example genes = c("YLR113W", "YFL026W") params = new("KEGGHyperGParams", geneIds = unique(genes), universeGeneIds = character(0), annotation = "YEAST", pvalueCutoff = 0.1, testDirection = "over") hgr.yeast.kegg = hyperGTest(params) --- PFAM and YEAST example genes = c("YLR113W", "YNR031C") params = new("PFAMHyperGParams", geneIds = unique(genes), universeGeneIds = character(0), annotation = "YEAST", pvalueCutoff = 0.1, testDirection = "over") hgr.yeast.pfam = hyperGTest (params) > Does this not work? > >> params = new("KEGGHyperGParams", geneIds = unique(genes), >> universeGeneIds = character(0), annotation = "YEAST", >> ontology = ontology, pvalueCutoff = pvalue, >> conditional = FALSE, >> testDirection = "over") >

ADD REPLY • link 17.1 years ago Paul Shannon ★ 1.1k

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Paul Shannon wrote: > With Seth's prompting :} I went back and fiddled a while longer with > my KEGGHyperGParams. I eventually found the right combination, which > I include below (along with a PFAMHyperGParams example) in case it > might be useful to someone. > > As for Seth's other comment: > >> (although I'm confused why specifying zero-length for universeGeneIds >> makes any sense...) > > I think it does make sense as long as the goal of the analysis is > annotation, > rather than enrichment. The Category package is a very handy way > to discover, for example, which GO terms, KEGG pathways, and > PFAM domains are shared among proteins, as I try to elucidate the > results of experiments in phosphoproteomics. > The GSEAbase package is I think a much better way to do that, and is actually intended for such purposes. best wishes Robert > > ---- KEGG and YEAST example > > genes = c("YLR113W", "YFL026W") > params = new("KEGGHyperGParams", geneIds = unique(genes), > universeGeneIds = character(0), annotation = "YEAST", > pvalueCutoff = 0.1, testDirection = "over") > > hgr.yeast.kegg = hyperGTest(params) > > --- PFAM and YEAST example > > genes = c("YLR113W", "YNR031C") > params = new("PFAMHyperGParams", geneIds = unique(genes), > universeGeneIds = character(0), annotation = "YEAST", > pvalueCutoff = 0.1, testDirection = "over") > > hgr.yeast.pfam = hyperGTest (params) > > >> Does this not work? >> >>> params = new("KEGGHyperGParams", geneIds = unique(genes), >>> universeGeneIds = character(0), annotation = "YEAST", >>> ontology = ontology, pvalueCutoff = pvalue, >>> conditional = FALSE, >>> testDirection = "over") > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

ADD REPLY • link 17.1 years ago rgentleman ★ 5.5k

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Hi Robert, Last week you wrote: The GSEAbase package is I think a much better way to do that, and is actually intended for such purposes. where the 'that' you refer to is is my use (abuse...) of the Category package to find shared GO categories, KEGG pathways, and PFAM domains among (typically) 30-100 proteins identified by shotgun proteomics. I'm sorry to be so slow on the uptake here, but after reading the GSEAbase vignette, I am no closer to understanding how to do the GSEAbase equivalent of the following quick method for finding that two of my proteins share the PF00069 domain: proteins = c ("YLR113W", "YBR069C", "YBR279W", "YCR030C", "YDR168W", "YNR031C") params = new ("PFAMHyperGParams", geneIds = proteins, universeGeneIds = character(0), annotation = "YEAST", pvalueCutoff = 1.0, testDirection = "over") hgr.yeast.pfam = hyperGTest (params) subset (summary (hgr.yeast.pfam), Count >= 2) PFAMID Pvalue OddsRatio ExpCount Count Size Term PF00069 PF00069 0.006570706 24.98214 0.1321280 2 114 PF00069 Is there an example you could refer me to? Thanks! - Paul >> The Category package is a very handy way >> to discover, for example, which GO terms, KEGG pathways, and >> PFAM domains are shared among proteins, as I try to elucidate the >> results of experiments in phosphoproteomics. > The GSEAbase package is I think a much better way to do that, and > is actually intended for such purposes.

ADD REPLY • link 17.1 years ago Paul Shannon ★ 1.1k

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Hi Paul, Paul Shannon wrote: > Hi Robert, > > Last week you wrote: > > The GSEAbase package is I think a much better way to do that, and is > actually intended for such purposes. > > where the 'that' you refer to is is my use (abuse...) of the Category > package to find shared GO categories, KEGG pathways, and PFAM domains among > (typically) 30-100 proteins identified by shotgun proteomics. > Yes, that is what I was referring to. But perhaps we can make sure that we are both talking about the same thing. If what you want is the incidence matrix, say, rows correspond to yeast orfs, and columns to Pfam domains, with entries 1 or 0, depeding on whether the gene/orf has the domain, then GSEABase is a better alternative than performing hypergeomtetric testing. If that is what you want, let me know and I will post some code, and if not, maybe you could explain more about what you do want. I find it helpful if you give the overall goal, not the immediate one. thanks Robert > I'm sorry to be so slow on the uptake here, but after reading the > GSEAbase vignette, > I am no closer to understanding how to do the GSEAbase equivalent of the > following > quick method for finding that two of my proteins share the PF00069 domain: > > proteins = c ("YLR113W", "YBR069C", "YBR279W", "YCR030C", "YDR168W", > "YNR031C") > > params = new ("PFAMHyperGParams", geneIds = proteins, > universeGeneIds = character(0), annotation = "YEAST", > pvalueCutoff = 1.0, testDirection = "over") > > hgr.yeast.pfam = hyperGTest (params) > > subset (summary (hgr.yeast.pfam), Count >= 2) > > PFAMID Pvalue OddsRatio ExpCount Count Size Term > PF00069 PF00069 0.006570706 24.98214 0.1321280 2 114 PF00069 > > > Is there an example you could refer me to? > > Thanks! > > - Paul > > > > > >>> The Category package is a very handy way >>> to discover, for example, which GO terms, KEGG pathways, and >>> PFAM domains are shared among proteins, as I try to elucidate the >>> results of experiments in phosphoproteomics. >> The GSEAbase package is I think a much better way to do that, and is >> actually intended for such purposes. > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

ADD REPLY • link 17.1 years ago rgentleman ★ 5.5k

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