getSinglePhasedSNPPrevalence: Compute the cellular prevalence of each group of cells

In chedonat/OncoPhase: SOMATIC MUTATION CELLULAR PREVALENCE COMPUTATION

Description

This is a generic function to compute the detailed prevalence of a single mutation using the linear system of the model.

Usage

getSinglePhasedSNPPrevalence(varcounts_snv, refcounts_snv, major_cn, minor_cn,
  varcounts_snp, refcounts_snp, context, Trace = FALSE,
  LocusCoverage = TRUE, NormalCellContamination = NULL)

Arguments

varcounts_snv	A count of alleles supporting the variant sequence of the somatic mutation
refcounts_snv	A count of alleles supporting the reference sequence of the somatic mutation
major_cn	major copy number at the locus of the mutation
minor_cn	minor copy number (or a vector of copy number if multiple tumor samples)
varcounts_snp	A count of alleles supporting the variant sequence of the Germline SNP
refcounts_snp	A count of alleles supporting the reference sequence of the Germline SNP
context	represents either the situation of a mutation which occurred after the CNV ("C1") or the context of a mutation which occurred before the CNV ("C2"). If not provided, the right context will be estimated from the input
Trace	Print a trace of the eecution.
LocusCoverage	when set to TRUE, the SNV locus coverage is estimated to the average coverage of the phased SNP and the variant allele fraction is the ratio of the variant allele count over the estimated locus coverage.
NormalCellContamination	If provided, represents the rate of normal cells contaminations in the experiment.

Value

A list of the three cellular prevalence of each of the three groups of cells

See Also

getPrevalence, getMatricesPhasedSNP

Examples

Prevalences = getSinglePhasedSNPPrevalence(3, 10,2,1,8,5,"C1")

 print(Prevalences)
# Germ  Alt Both
# 0.4  0.0  0.6

chedonat/OncoPhase documentation built on May 13, 2019, 3:39 p.m.