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All functions

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