Defining a single clone using multiple variants. — ClonalDefinition

This function defines a single clone using a set of variants. A cell is considered to be part of the clone, if it has all of the provided variants. A maximum number of missing variants can be set.

Usage

ClonalDefinition_Singular(
  se,
  variants,
  dropout = FALSE,
  variants_essential = NULL,
  variants_excluding = NULL,
  min_vaf = 0.01,
  clone_name = "SingularClone",
  verbose = TRUE
)

Arguments

se: SummarizedExperiment object.
variants: Set of variants for clonal definition.
dropout: The number of missing variants allowed.
variants_essential: Which variants are considered essential? These will not be dropped if dropout is not NULL. The values can either be the variants names as character or indices for variants. A list of the same length as variants.
variants_excluding: Which variants are not allowed in the clone? Variants names. A list of the same length as variants.
min_vaf: Minimum VAF for a cell to be considered positive.
clone_name: What is the name of the clone? Default: SingularClone
verbose: Should the function be verbose? Default = TRUE