Determining the clonal diversity. — ClonalDiversity • sigurd

This function determines the clonal diversity. The clones are defined using the function ClonalDefinition. It is not required to use clones, but any column in the column data of the object can be used.

Usage

ClonalDiversity(
  se,
  grouping = "Clones",
  cells = NULL,
  diversity_measure = "EffectiveSpecies",
  base = exp(1),
  verbose = TRUE
)

Arguments

se: SummarizedExperiment object.
grouping: The meta data column used.
cells: Which cells should be used? NULL uses all cells.
diversity_measure: What diversity measure should be calculated? Can be EffectiveSpecies, shannon, simpson, invsimpson
base: The base for the diversity
verbose: Should the function be verbose? Default = TRUE