Function reference • CHOIR

All functions

CHOIR(): Run CHOIR clustering

CHOIRpalette(): Generate color palette

buildParentTree(): Build parent clustering tree

buildTree(): Build full hierarchical clustering tree

combineTrees(): Compile separately pruned clustering trees and standardize thresholds

compareClusters(): Compare any two clusters using CHOIR's random forest classifier permutation testing approach

getRecords(): Retrieve all CHOIR metadata

inferTree(): Infer clustering tree from pre-generated clusters

plotCHOIR(): Dimensional reduction plot with CHOIR clusters labeled

pruneTree(): Prune clustering tree using random forest classifiers

runCHOIRumap(): Run UMAP on CHOIR dimensionality reductions

runCountSplit(): Run countsplitting