CellularitiesFromFreq: Cellularities from allele frequency

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

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

QuantumClone documentation built on May 2, 2019, 3:03 a.m.