getMatricesSNVOnly: Generate the matrices C, W and M from a set of parameters...

In chedonat/OncoPhase: SOMATIC MUTATION CELLULAR PREVALENCE COMPUTATION

Description

This is a generic function to generate the matrices of the linear system (see the paper) from the allele counts and the copy number information under the SNVOnly mode.

Usage

getMatricesSNVOnly(varcounts_snv, refcounts_snv, major_cn, minor_cn, context,
  sigma = 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 at the locus of the mutation
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	Copy number of the parental chromosome harboring the mutation.

Value

the matrices W, C and M for the linear system of prevalence computation.

Examples

Matrices = getMatricesSNVOnly(3,10,2,1,"C1")

print(Matrices)
#$context
#[1] "C1"
#
#$W
#SNV
#SNV 0.2307692
#
#$M
#Germ Alt Both
#SNV    0   0    1
#
#$C
#Germ Alt Both
#SNV    2   3    3

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