gagblup: Genetic algorithm assisted genomic best liner unbiased...

In GAGBLUP: Genetic Algorithm Assisted Genomic Best Liner Unbiased Prediction

Genetic algorithm assisted genomic best liner unbiased prediction for genomic selection

Description

Performs genomic selection with genetic algorithm assisted genomic best liner unbiased prediction

Usage

gagblup(
  genotype,
  phenotype,
  fit_fun = "HAT",
  maxiter = 2000,
  nfold = 10,
  nTimes = 1,
  seed = 123,
  n_core = 1
)

Arguments

genotype	a matrix for genotypes in numeric format, with individuals in rows and markers in cols.
phenotype	a vector of phenotype, missing (NA) values are not allowed.
fit_fun	the fitness function. There are four options: fitness = "AIC"/"BIC"/"FIT"/"HAT", default is "HAT"
maxiter	max number of iterations for GAGBLUP, default is 2000
nfold	the number of folds. Default is 10.
nTimes	the number of independent replicates for the cross-validation. Default is 1.
seed	the random number. Default is 123.
n_core	the number of CPU to be used, default is 1.

Value

A list with following information is returned: $R2 the squared pearson correlation coefficient between the true value and the predicted value, $predicted_value the predicted value and the true value of the phenotype, $marker_selection a vector of the selected markers, with 1 indicates selected, 0 indicates not selected.

Examples

## load example data from GAGBLUP package
data(phenotype)
data(bins)
phenotype <- phenotype[1:200,3]
result <- gagblup(bins[1:200,],phenotype,fit_fun='HAT',maxiter=1,nfold=2,nTimes=1,seed=123,n_core=1)

GAGBLUP documentation built on Sept. 8, 2023, 5:47 p.m.