getSingleSNVOnlyPrevalence: Compute the cellular prevalence of each group of cells in...

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 making the model.

Usage

getSingleSNVOnlyPrevalence(varcounts_snv, refcounts_snv, major_cn, minor_cn,
  context, sigma = NULL, Trace = FALSE, 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)
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
sigma	The parental copy number of the chromosome harboring the mutation locus. Only needed if the context = C2. Should be either the major copy number either minor copy number
Trace	If TRUE, a trace of the execution will be printed
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, getMatricesSNVOnly

Examples

Prevalences = getSingleSNVOnlyPrevalence(3,10,2,1,"C2",2)

print(Prevalences)
#Germ      Alt     Both solutionNorm
#0.60     0.31     0.09     0.00

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