gaston2neiGWAS {rNeighborGWAS} | R Documentation |
Convert 'gaston' package's bed.matrix data to rNeighborGWAS genotype data.
Description
A function convert a bed.matrix dataset to rNeighborGWAS genotype data.
Usage
gaston2neiGWAS(x)
Arguments
x |
A 'bed.matrix' created using the |
Details
This function converts genotype data into -1, 0, or 1 digit as the rNeighborGWAS format. Zero indicates heterozygotes.
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
Author(s)
Yasuhiro Sato (sato.yasuhiro.36c@kyoto-u.jp)
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)