QuantumClone (version 1.0.0.6)

CellularitiesFromFreq: Cellularities from allele frequency

Description

Creates all possibilities for one mutation in one sample (given a genotype), then computes the cellularity associated with each possibility and finally the probability of each possibility

Usage

CellularitiesFromFreq(chr, position, Alt, Depth, Freec_ratio = NULL,
  Genotype = NULL, subclone.genotype = NULL, subclone.cell = NULL,
  contamination, restrict.to.AB = FALSE, force.single.copy = FALSE)

Arguments

chr

The chromosome on which is the position (numeric value, not chr1 as in BED files)

position

The genomic position of the mutation

Alt

Number of reads supporting the variation

Depth

Number of reads mapped at the position

Freec_ratio

The FREEC output associated with the sample of interest

Genotype

If the FREEC output is not given, the genotype associated with the locus (for example AAB)

subclone.genotype

If existing, the genotype of the subclone. Else NULL

subclone.cell

The cellular prevalence of the subclone which has a different Copy Number at this site

contamination

The fraction of normal cells in the sample

restrict.to.AB

Should the analysis keep only sites located in A and AB sites in all samples?

force.single.copy

Should all mutations in overdiploid regions set to single copy? Default is FALSE