Writes a Pop-class to PLINK PED and MAP files. The arguments
for this function were chosen for consistency with
RRBLUP2. The base pair coordinate will the locus
position as stored in AlphaSimR and not an actual base pair
position. This is because AlphaSimR doesn't track base pair
positions, only relative positions for the loci used in the
simulation.
Usage
writePlink(
pop,
baseName,
traits = 1,
use = "pheno",
snpChip = 1,
useQtl = FALSE,
simParam = NULL,
...
)Arguments
- pop
an object of
Pop-class- baseName
basename for PED and MAP files.
- traits
an integer indicating the trait to write, a trait name, or a function of the traits returning a single value.
- use
what to use for PLINK's phenotype field. Either phenotypes "pheno", genetic values "gv", estimated breeding values "ebv", breeding values "bv", or random values "rand".
- snpChip
an integer indicating which SNP chip genotype to use
- useQtl
should QTL genotypes be used instead of a SNP chip. If TRUE, snpChip specifies which trait's QTL to use, and thus these QTL may not match the QTL underlying the phenotype supplied in traits.
- simParam
an object of
SimParam- ...
additional arguments if using a function for traits