Reference

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

lcvqe()

LCVQE algorithm.

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