pvdiv_autoSVD: Wrapper for the snp_autoSVD function for switchgrass.
In Alice-MacQueen/switchgrassGWAS: Genome Wide Association on Panicum virgatum

Description Usage Arguments Value Examples

This is a wrapper to determine population structure for GWAS for a SNP file with the switchgrass chromosomes, which are not numeric. Arguments that are recognized by bigsnpr::snp_autoSVD can also be specified in this function.

1	pvdiv_autoSVD(snp, k = 10, ncores = 1, saveoutput = FALSE, ...)

`snp`	A "bigSNP" object; load with bigsnpr::snp_attach().
`k`	Integer. The number of principal components to find. Default is 10.
`ncores`	Integer. Number of cores to use. Default is one.
`saveoutput`	Logical. Should the output be saved to the working directory?
`...`	Other arguments to `snp_autoSVD`.

A big_SVD object.

snpfile <- system.file("extdata", "example_bigsnp.rds", package = "switchgrassGWAS")
library(bigsnpr)
snp <- snp_attach(snpfile)
svd5 <- pvdiv_autoSVD(snp = snp, k = 5, saveoutput = FALSE)