Description Usage Arguments Value Examples
View source: R/pvdiv_standard_gwas.R
Calculate the kinship matrix using code from GAPIT and bigsnpr and the methods of VanRaden (2009, J. Dairy Sci. 91:4414???C4423). Note that this matrix cannot currently be used with the GWAS methods in bigsnpr; however, this matrix could be used with other GWAS programs.
1 | pvdiv_kinship(snp, ind.row = NA, hasInbred = TRUE, saveoutput = FALSE)
|
snp |
A "bigSNP" object; load with bigsnpr::snp_attach(). |
ind.row |
An integer vector of the rows (individuals) to find a kinship matrix for. Defaults to all rows. |
hasInbred |
Logical. Does the SNP file contain inbred individuals or closely related individuals, like siblings? |
saveoutput |
Logical. Should the output be saved to the working directory? |
A kinship matrix with labeled rows and columns.
1 2 3 4 | snpfile <- system.file("extdata", "example_bigsnp.rds", package = "switchgrassGWAS")
library(bigsnpr)
snp <- snp_attach(snpfile)
K <- pvdiv_kinship(snp = snp, saveoutput = FALSE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.