mle_p {mbmixture}

MLE of p for fixed e

Description

Calculate the MLE of the contaminant probability p for a fixed value of the sequencing error rate e.

Usage

mle_p(
  tab,
  e = 0.002,
  interval = c(0, 1),
  tol = 0.000001,
  check_boundary = FALSE
)

Arguments

tab

Dataset of read counts as 3d array of size 3x3x2, genotype in first sample x genotype in second sample x allele in read.

e

Assumed value for the sequencing error rate

interval

Interval to which each parameter should be constrained

tol

Tolerance for convergence

check_boundary

If TRUE, explicitly check the boundaries of interval.

Value

A single numeric value, the MLE of p, with the log likelihood as an attribute.

Examples

data(mbmixdata)
mle_p(mbmixdata, e=0.002)