writePlink {AlphaSimR}

Writes a Pop-class as PLINK files

Description

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

Examples

## Not run: 
#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)

#Set simulation parameters
SP = SimParam$new(founderPop)
\dontshow{SP$nThreads = 1L}
SP$setSexes(sex="yes_rand")
SP$addTraitA(nQtlPerChr=10)
SP$addSnpChip(nSnpPerChr=5)
SP$setVarE(h2=0.5)

#Create population
pop = newPop(rawPop = founderPop)

# Write out PLINK files
writePlink(pop, baseName="test")

## End(Not run)