Defining clones.

This function defines clones using a combination of variants supplied. Each set of variants can be and should be paired with a identity, like sample or cell type. The clones are then only determined in respect to this group. If this information is not provided, the clones are determined for all cells present.

Usage

ClonalDefinition(
  se,
  variants_ls,
  grouping = NULL,
  identities = NULL,
  verbose = TRUE
)

Arguments

se

SummarizedExperiment object.

variants_ls

List of variants for clonal definition

grouping

The meta data column used to split the cells into groups. Default = NULL

identities

Vector of groups, like samples.

verbose

Should the function be verbose? Default = TRUE