git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@100882 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 19/03/2015 17:51:53
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 05/02/2013 22:15:53
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new file mode 100644 |
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+import(Biobase) |
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+ |
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+ |
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+exportClasses( |
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+ IcaSet, MineICAParams |
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+) |
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+ |
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+exportMethods( |
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+ dat, "dat<-", datByGene, "datByGene<-", nbComp, organism, "organism<-", A, Alist, "A<-", S, "S<-", SByGene, "SByGene<-", SByGene, "SByGene<-", |
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+ "[", "[<-", getComp, indComp, "indComp<-", compNames, "compNames<-", "witGenes<-", witGenes, Slist, SlistByGene, |
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+ chipVersion, "chipVersion<-", "chipManu<-", chipManu, "refSamples<-", refSamples, "typeID<-", typeID, |
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+annotfile, "annotfile<-", Afile, "Afile<-", Sfile, "Sfile<-", datfile, "datfile<-", resPath, "resPath<-", genesPath, "genesPath<-", annot2col, "annot2col<-", selCutoff, "selCutoff<-", pvalCutoff, "pvalCutoff<-", geneNames, mart, "mart<-" |
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+ |
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+) |
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+ |
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+export(annot2Color) |
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+export(annotFeatures) |
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+export(annotFeaturesComp) |
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+export(annotFeaturesWithBiomaRt) |
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+export(annotInGene) |
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+export(annotReciprocal) |
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+export(buildIcaSet) |
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+export(buildMineICAParams) |
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+export(clusterFastICARuns) |
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+export(clusterSamplesByComp) |
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+export(clusterSamplesByComp_multiple) |
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+export(clusVarAnalysis) |
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+export(compareAn) |
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+export(compareAn2graphfile) |
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+export(compareGenes) |
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+export(cor2An) |
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+export(getProj) |
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+export(getSdExpr) |
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+export(hypergeoAn) |
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+export(nbOccInComp) |
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+export(nodeAttrs) |
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+export(plotAllMix) |
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+export(plotCorGraph) |
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+export(plot_heatmapsOnSel) |
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+export(plotMix) |
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+export(plotPosAnnotInComp) |
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+export(plotPosSamplesInComp) |
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+export(qualVarAnalysis) |
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+export(quantVarAnalysis) |
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+export(relativePath) |
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+export(runAn) |
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+export(runCompareIcaSets) |
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+export(runEnrich) |
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+export(runICA) |
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+export(selectContrib) |
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+export(selectFeatures_IQR) |
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+export(selectWitnessGenes) |
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+export(writeGenes) |
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+export(writeHtmlResTestsByAnnot) |
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+export(writeProjByComp) |
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+export(writeRnkFiles) |