ClonalDiversity: Determining the clonal diversity.

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

Determining the clonal diversity.

Description

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

CostaLab/sigurd documentation built on Feb. 10, 2025, 11:08 p.m.