hap.control: Control for haplotype reconstruction
In gap: Genetic Analysis Package

hap.control

R Documentation

Control for haplotype reconstruction

Description

Control for haplotype reconstruction

Usage

hap.control(
  mb = 0,
  pr = 0,
  po = 0.001,
  to = 0.001,
  th = 1,
  maxit = 100,
  n = 0,
  ss = 0,
  rs = 0,
  rp = 0,
  ro = 0,
  rv = 0,
  sd = 0,
  mm = 0,
  mi = 0,
  mc = 50,
  ds = 0.1,
  de = 0,
  q = 0,
  hapfile = "hap.out",
  assignfile = "assign.out"
)

Arguments

`mb`	Maximum dynamic storage to be allocated, in Mb.
`pr`	Prior (ie population) probability threshold.
`po`	Posterior probability threshold.
`to`	Log-likelihood convergence tolerance.
`th`	Posterior probability threshold for output.
`maxit`	Maximum EM iteration.
`n`	Force numeric allele coding (1/2) on output (off).
`ss`	Tab-delimited speadsheet file output (off).
`rs`	Random starting points for each EM iteration (off).
`rp`	Restart from random prior probabilities.
`ro`	Loci added in random order (off).
`rv`	Loci added in reverse order (off).
`sd`	Set seed for random number generator (use date+time).
`mm`	Repeat final maximization multiple times.
`mi`	Create multiple imputed datasets. If set >0.
`mc`	Number of MCMC steps between samples.
`ds`	Starting value of Dirichlet prior parameter.
`de`	Finishing value of Dirichlet prior parameter.
`q`	Quiet operation (off).
`hapfile`	a file for haplotype frequencies.
`assignfile`	a file for haplotype assignment.