dot-estimateQ: EM algorithm to calculate q

In SunPathLab/Butte: BoUnds of Time Till Expansion, inferring the SCNA arrival time in the somatic evolution toward the most recent common ancestor of tumor sample(s).

EM algorithm to calculate q

Description

Estimate the proportion the proportions of SSNVs at each allele state from sequencing data.

Usage

.estimateQ(
  x,
  m,
  alleleSet,
  alleleFreq = NULL,
  history,
  type = c("identifiable", "butte"),
  init = NULL,
  maxiter = 100,
  tol = 1e-04,
  xGreaterZero = TRUE,
  useGradient = FALSE
)

Arguments

x	vector of number of reads supporting SSNVs
m	vector of total read depth for SSNVs
alleleSet	vector of possible allele frequencies
alleleFreq	the observed allele frequencies
history	a list of possible evolutionary history matrices, see also function "cnmutHistory"
type	set it to be either "identifiable" or "butte"
init	the initial values of vector q (probability of a randomly acquired SSNV having each allele state)
maxiter	maximum number of iterations in calculation q
tol	the tolerance in the convergence of q
xGreaterZero	determines whether the likelihood will account for the fact that only observe SSNVs with mutant read count x[i] > 0

Value

A list of possible matrices

SunPathLab/Butte documentation built on Sept. 19, 2023, 9:42 a.m.