Function reference
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K2colData()`K2colData<-`() - Data frame of phenotypic information from K2 object
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K2dashboard() - Generate interactive dashboard of K2 Taxonomer results
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K2data()`K2data<-`() - Data matrix from K2 object
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K2dendro() - Reformat K2Taxonomer results to dendrogram object
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K2eMat()`K2eMat<-`() - Expression matrix object used in partitioning
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K2eMatDS()`K2eMatDS<-`() - Expression matrix object used for differential expression
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K2gMat()`K2gMat<-`() - Numeric matrix of enrichment scores
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K2gene2Pathway()`K2gene2Pathway<-`() - Vector of collapsed pathways for which each gene belongs
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K2geneURL()`K2geneURL<-`() - Assign URLs to genes included in K2Taxonomer run
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K2genesetURL()`K2genesetURL<-`() - Assign URLs to genesets included in K2Taxonomer run
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K2genesets()`K2genesets<-`() - Named list of genesets used in K2Taxonomer run
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K2meta()`K2meta<-`() - Meta data defining parameters of K2Taxonomer run
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K2preproc() - Function to create K2 object for pre-processing
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K2res - Example K2Taxonomer output
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K2results()`K2results<-`() - Annotated list of partition assignments from K2Taxonomer run
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K2tax() - Function to K2 Taxonomer partitioning
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K2visNetwork() - Interactive K2 dendrogram
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aggregateGeneSetScores() - Take difference of two paired bi-directional gene set scores
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cKmeansDownsampleSmallest() - Wrapper for constrained K-means on data subsampled to the smallest cohort size.
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cKmeansDownsampleSqrt() - Wrapper for constrained K-means on data subsampled to the square root of the number of observations in each cohort.
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getDGEInter() - Create interactive table of differential gene expression analysis results from 'K2' object
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getDGETable() - Extract table of differential results from 'K2' object
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getEnrichmentInter() - Create interactive table of gene set enrichment results from 'K2' object
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getEnrichmentTable() - Extract table of enrichment results from 'K2' object
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getGenePathways() - Map features (genes) to feature list (genesets)
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hclustWrapper() - Wrapper for hierarchical clustering
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matrixORdgCMatrix-class - K2 object
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plotGenePathway() - Plot gene expression or enrichment scores
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runDGEmods() - Perform differential analysis between subgroups at each partition
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runDSSEmods() - Perform differential analysis of enrichment scores between subgroups at each partition
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runFISHERmods() - Perform Fisher test overrepresentation analysis of each subgroup
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runScoreGeneSets() - Enrichment scoring of gene sets on expression data