rNeighborGWAS (version 1.2.4)

gaston2neiGWAS: Convert gaston's bed.matrix data to rNeighborGWAS genotype data.

Description

A function convert a bed.matrix dataset to rNeighborGWAS genotype data.

Usage

gaston2neiGWAS(x)

Value

A list including an individual x marker matrix, a data.frame including chromosome numbers in the first column, and SNP positions in the second column, and a numeric vector including phenotypes for individuals.

• geno Individual x marker matrix

• gmap Data.frame including chromosome numbers in the first column, and SNP positions in the second column

• pheno Numeric vector including phenotypes for individuals

Arguments

x

A bed.matrix created using the gaston package (Perdry & Dandine-Roulland 2020).

Author

Yasuhiro Sato ()

Details

This function converts genotype data into -1, 0, or 1 digit as the rNeighborGWAS format. Zero indicates heterozygotes.

References

Perdry H, Dandine-Roulland C. (2020) gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models. https://CRAN.R-project.org/package=gaston

Examples

data("TTN", package="gaston")
x <- gaston::as.bed.matrix(TTN.gen, TTN.fam, TTN.bim)
g <- gaston2neiGWAS(x)