Description Usage Arguments Value Examples
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.
1 2 | getMatricesPhasedSNP(varcounts_snv, refcounts_snv, major_cn, minor_cn,
varcounts_snp, refcounts_snp, context, LocusCoverage = FALSE)
|
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. |
the matrices W, C and M for the linear system of prevalence computation.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.