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

Description Usage Arguments Value See Also Examples

Description

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

Usage

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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

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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.