mle_e: MLE of e for fixed p

In kbroman/mbmixture: Microbiome Mixture Analysis

MLE of e for fixed p

Description

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

Usage

mle_e(
  tab,
  p = 0.05,
  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.
p	Assumed value for the contaminant probability
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 e, with the log likelihood as an attribute.

Examples

data(mbmixdata)
mle_e(mbmixdata, p=0.74)

kbroman/mbmixture documentation built on Nov. 28, 2024, 6:38 p.m.