empiricalBayesFuncs: Functions for performing empirical Bayesian calculations

In daynefiler/filer2020B: Analysis for DOI to be added

Description

Collection of functions for performing empirical Bayesian calculations

Usage

cfUpdateEmpGeno(mar, dep, empPMAR, empGenoFreq)

cfUpdateEmpPMAR(marVec, depVec, empGeno, ffPrior, ffPriorWt)

cfUpdateEmpGenoFreq(empGeno, qPrior, qPriorWt)

cfEmpGeno(
  marVec,
  depVec,
  qPrior,
  ffPrior,
  nchng = 5,
  its = 50,
  ffPriorWt = length(marVec)/5,
  qPriorWt = 1000,
  pltTrain = FALSE
)

Arguments

mar	Integer of length 1, minor allele read count
dep	Integer of length 1, total read depth
empPMAR	Named numeric, empirical estimates of expected PMAR values
empGenoFreq	Named numeric, empirical estimates of genotype pair frequencies
marVec	Integer, minor allele read counts
depVec	Integer, total read depths
empGeno	Character, empirical genotype calls
ffPrior	Numeric of length 1, fetal fraction prior
ffPriorWt	Numeric of length 1, the weight given to the fetal fraction prior
qPrior	Numeric of length 1, average minor allele frequency prior
qPriorWt	Numeric of length 1, the weight given to the q prior
pltTrain	Logical of length 1, plot genotypes at each training iteration when TRUE

Details

ffPriorWt can be thought of as the number of observations supportint the fetal fraction prior

Functions

• cfUpdateEmpGeno: Update the emperic genotype call

• cfUpdateEmpPMAR: Update the emperic PMAR values

• cfUpdateEmpGenoFreq: Update the emperic genotype frequencies

• cfEmpGeno: Make empiric genotype calls

daynefiler/filer2020B documentation built on Dec. 30, 2021, 8:44 a.m.