cancerCellFraction: Cancer cell fraction

In ndbrown6/CNtu: Copy Number tree utilities

Cancer cell fraction

Description

Computes the maximum likelihood estimate of cancer cell fractions given observed VAF

Usage

alpha_hat = cancercellFraction(f_hat, n, qt, q2, alpha, e=0.01)

Arguments

f_hat	numeric vector of variant allele fractions where f_hat = 0 … 1
n	integer vector of total depth of coverage
qt	integer vector of total copy numbers
q2	integer vector of major allele
alpha	numeric value of global purity where alpha = 0 … 1
e	numeric value of sequencing error rate where e = 0 … 1

Value

Data frame with columns as follows:

1. cell_multiplicity:

2. scaled_cell_frac:

3. cancer_cell_frac:

4. ccf_95CI_low:

5. ccf_95CI_high:

6. Pr_somatic_clonal: probability that SNV is somatic and clonal

7. Pr_germline: probability that SNV is a germline mutation

8. Pr_subclonal: probability that SNV is somatic and subclonal

9. Pr_subclonal_wt0: probability that SNV is subclonal when qt = 1, 0 otherwise

10. Pr_wt0: probability that q2 copies are mutated if locus has uniparental allele (qt = q2), 0 otherwise

11. Pr_ge2: warning: undocumented \& not in use

12. Pr_GL_som_HZ_alt: warning: undocumented \& not in use

13. Pr_GL_som_HZ_ref: warning: undocumented \& not in use

14. Pr_cryptic_SCNA: warning: undocumented

15. LL: log likelihood

16. sq: most probable number of mutated copies where sq = 1 ldots q2

17. Pr_somatic: probability that SNV is somatic i.e. Pr_somatic_clonal + Pr_subclonal

Author(s)

David Brown
[e-mail]

ndbrown6/CNtu documentation built on March 16, 2023, 1:01 a.m.