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.