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Defining clones.

ClonalDefinition.Rd

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,
  explicit = FALSE,
  explicit_not = NULL,
  explicit_min_vaf = 0.01,
  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.

explicit

Do you want to specify the variants forming a clone? Then the variant_ls needs to be a list of variants that each define a clone. One variant per group.

explicit_not

Do you want to specify a set of variants that the cell may not have? One set per group.

explicit_min_vaf

Minimum VAF for a cell to be considered positive.

verbose

Should the function be verbose? Default = TRUE