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