getCloneLikelihood: mutationCalls accessors

In benstory/mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

mutationCalls accessors

Description

Retrieves the full matrix of likelihoods associating single cells with clones

Usage

getCloneLikelihood(mutcall, mainClones = length(mutcall@mut2clone) > 0)

getMainClone(mutcall, mainClones = length(mutcall@mut2clone) > 0)

getConfidence(mutcall, mainClones = length(mutcall@mut2clone) > 0)

getMut2Clone(mutcall)

Arguments

mutcall	object of class mutationCalls.
mainClones	Retrieve likelihoods associated with the main Clones. Defaults to TRUE if clusterMetaclones has been run.

Value

Return TRUE if clusterMetaclones has been run otherwise returns the cell by clone matrix of likelihood associating each cell to a given clone.

Functions

• getMainClone: Retrieve the most likely clone associate with each cell.

• getConfidence: Retrieve the likelihood of the most likely clone for each cell.

• getMut2Clone: Retrieve the assignment of mutations to clones, once clusterMetaclones has been run.

Examples

load(system.file("extdata/LudwigFig7.Rda",package =
"mitoClone2"))
likelihood_matrix <- getCloneLikelihood(LudwigFig7)

benstory/mitoClone2 documentation built on Nov. 8, 2023, 12:13 a.m.