gap (version 1.6)

hap.control: 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"
)

Value

A list containing the parameter specifications to the function.

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.