ClonalDefinition: Defining clones.

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

Defining clones.

Description

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

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