getMatricesPhasedSNP: 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.

Usage

getMatricesPhasedSNP(varcounts_snv, refcounts_snv, major_cn, minor_cn,
  varcounts_snp, refcounts_snp, context, LocusCoverage = FALSE)

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
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
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.

Value

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

Examples

Matrices = getMatricesPhasedSNP(3, 10,2,1,8,5,"C1")

print(Matrices)
#$context
#[1] "C1"
#
#$W
#          SNP       SNV
#SNP 0.6153846 0.0000000
#SNV 0.0000000 0.2307692
#
#$M
#    Germ Alt Both
#SNP    1   2    2
#SNV    0   0    1
#
#$C
#    Germ Alt Both
#SNP    2   3    3
#SNV    2   3    3

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