mutatedCopies: Predicts the number of mutated copies

In ndbrown6/CNtu: Copy Number tree utilities

Predicts the number of mutated copies

Description

Computes the maximum likelihood estimate of the number of mutated copies given the observed VAF

Usage

sq_hat = mutatedCopies(f_hat, n, qt, q2, alpha, e, d)

Arguments

f_hat	numeric vector of observed VAF where f_hat = 0 … 1
n	integer vector of total number of reads covering mutated loci
qt	integer vector of total copy numbers
q2	integer vector of major allele counts
alpha	numeric for the global cellular fraction where alpha = 0 … 1
e	numeric for expected sequencing error where e = 0 … 1
d	character string for the underlying distribution 'beta' or 'binomial'

Value

Integer vector of estimates of mutated copies

Author(s)

David Brown
[e-mail]

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