Probability.to.belong.to.clone: Probability

In DeveauP/QuantumClone: Clustering Mutations using High Throughput Sequencing (HTS) Data

Description

Returns dataframe with all informations about mutation (Number of copies, Cellularity, etc.) and probability to belong to a clone

Usage

Probability.to.belong.to.clone(
  SNV_list,
  clone_prevalence,
  contamination,
  clone_weights = NULL
)

Arguments

SNV_list	A list of dataframes (one for each sample), with as columns : (for the first column of the first sample the name of the sample), the chromosome "Chr",the position of the mutation "Start", the number of reads supporting the mutation "Alt", the depth of coverage at this locus "Depth", and if the output from FREEC for the samples are not associated, the genotype "Genotype".
clone_prevalence	List of numeric vectors giving the cellular prevalence of each clone in each sample, not normalized for contamination. This should be stored in 'QC_output$EM.output$centers'
contamination	Numeric vector giving the contamination by normal cells
clone_weights	Numeric vector giving the proportion of mutations in each clone

Value

list of items allowing to attribute variant to a cluster

Examples

set.seed(123)
SNVs<-QuantumCat(number_of_clones = 2,number_of_mutations = 50,number_of_samples = 1,ploidy = "AB")
Probability.to.belong.to.clone(SNV_list=SNVs,
clone_prevalence=list(c(0.5,1),c(0.5,1)),contamination=c(0,0))

DeveauP/QuantumClone documentation built on Oct. 29, 2021, 8:56 a.m.