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K2-class
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K2 object |
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K2dashboard()
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Generate interactive dashboard of K2 Taxonomer results |
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K2data() `K2data<-`()
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Data matrix from K2 object |
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K2dendro()
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Reformat K2Taxonomer results to dendrogram object |
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K2eSet() `K2eSet<-`()
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ExpressionSet object used in K2Taxonomer run |
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K2gSet() `K2gSet<-`()
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ExpressionSet object of of GSVA output |
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K2gene2Pathway() `K2gene2Pathway<-`()
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Vector of collapsed pathways for which each gene belongs |
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K2geneURL() `K2geneURL<-`()
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Assign URLs to genes included in K2Taxonomer run |
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K2genesetURL() `K2genesetURL<-`()
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Assign URLs to genesets included in K2Taxonomer run |
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K2genesets() `K2genesets<-`()
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Named list of genesets used in K2Taxonomer run |
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K2info() `K2info<-`()
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Data frame of phenotypic information from K2 object |
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K2meta() `K2meta<-`()
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Meta data defining parameters of K2Taxonomer run |
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K2preproc()
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Function to create K2 object for pre-processing |
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K2res
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Example K2Taxonomer output |
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K2results() `K2results<-`()
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Annotated list of partition assignments from K2Taxonomer run |
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K2tax()
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Function K2 Taxonomer |
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K2visNetwork()
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Interactive K2 dendrogram |
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aggregateGSVAscores()
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Take difference of two paired GSVA scores |
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cKmeansWrapper()
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Wrapper for constrained K-means |
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cKmeansWrapperSubsample()
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Wrapper for constrained K-means on subsampled data |
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getDGETable()
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Extract table of differential results from 'K2' object |
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getEnrichmentTable()
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Extract table of enrichment results from 'K2' object |
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getGenePathways()
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Map features (genes) to feature list (genesets) |
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getTestsModTable()
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Extract table of phenotypic variable tests from 'K2' object |
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hclustWrapper()
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Wrapper for hierarchical clustering |
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runDGEmods()
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Perform differential analysis of gene splits |
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runDSSEmods()
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Perform differential analysis of single-sample gene set enrichment |
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runGSEmods()
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Perform hyperenrichment of split specific gene signatures |
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runGSVAmods()
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Perform ssGSVA on gene sets and get set signature hits |
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runK2Taxonomer()
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Wrapper function to run K2Taxonomer algorithm and annotation |
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runTestsMods()
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Perform tests to test for associations between subgroups and
phenotypic variables |