fFixQN: quasi-Newton when f is fixed

In radmixture: Calculate Population Stratification

Description

quasi-Newton for ancestry analysis when F is fixed

Usage

fFixQN(gnew, qnew, f, tol, method, pubdata)

Arguments

gnew	Integer which length is the number of SNPs used in calculation.
qnew	Initial q used in calculation. A vector. sum(q) must be 1.
f	Allele frequencies learned from the reference panels.
tol	Tolerance, the default value is 1e-4.
method	Choose which algorithm you want to use. EM or BR.
pubdata	You can choose a public dataset here, E11, K13, K4, K12b, K7b, World9. You also can use other public dataset which is not in this package.

Value

Estimation results of q and the loglikelihood value of each iteration.

Examples

## res <- tfrdpub(genotype, 4, globe4.alleles, globe4.4.F)
## ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = 'BR', pubdata = 'K4')

Example output

radmixture documentation built on May 2, 2019, 6:11 a.m.