hap.control | R Documentation |
Control for haplotype reconstruction
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"
)
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. |
A list containing the parameter specifications to the function.
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