qpadm_wrapper: Wrapper function around the original qpAdm program

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Wrapper function around the original qpAdm program

Description

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

Usage

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

## Not run: 
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')

## End(Not run)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.