Wrapper function around the original qpAdm program

This requires a working installation of qpAdm, which will be called using system

qpadm_wrapper(
  pref,
  left,
  right,
  target = NULL,
  bin = "~np29/o2bin/qpAdm",
  outdir = "./",
  parfile = NULL,
  allsnps = "NO",
  blgsize = 0.05,
  fancyf4 = "NO",
  f4mode = "YES",
  inbreed = "NO",
  printonly = FALSE,
  env = "",
  verbose = TRUE
)

Arguments

pref: Path to and prefix of the packedancestrymap genotype files
left: Left populations (or leftlist file)
right: Right populations (or rightlist file)
target: Target population
bin: Path to the qpAdm binary file
outdir: Output directory. files out, parfile, leftlist, rightlist will be overwritten
parfile: qpAdm parameter file
allsnps: allsnps
blgsize: blgsize
fancyf4: fancyf4
f4mode: f4mode
inbreed: inbreed
printonly: Should the command be printed or executed?
env: Export environmental variables. See examples.
verbose: Print progress updates

Value

If not printonly, a data frame with parsed qpAdm output

Examples

if (FALSE) {
left = c('Altai_Neanderthal.DG', 'Vindija.DG')
right = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG', 'Switzerland_Bichon.SG')
target = 'Denisova.DG'
qpadm_wrapper('genotype_prefix', left, right, target,
  bin = 'path/to/qpAdm')
}