bin: Binning Genotypes for Dimensional Reduction

In GAGBLUP: Genetic Algorithm Assisted Genomic Best Liner Unbiased Prediction

Binning Genotypes for Dimensional Reduction

Description

Binning the original genotypes into bins for dimensional reduction under the principle of linkage disequilibrium.

Usage

bin(genotype = genotype, binvar = 0.15)

Arguments

genotype	a matrix for genotypes in numeric format, coded as 1, 0 and -1, with individuals in rows and markers in cols.
binvar	a hyper-parameter between 0 and 1, the closer to 0, the fewer bins yields. Users can choose binvar based on the required number of bins, default is 0.15.

Value

A list with following information is returned: $bins_genotypes binned genotypes $bins_range start and stop of each bin

Examples

## load example data from GAGBLUP package
data(genotype)
## binning genotypes
bins <- bin(genotype,0.2)
 

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