qpf4ratio_wrapper: Wrapper function around the original qpF4ratio program

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Wrapper function around the original qpF4ratio program

Description

This requires a working installation of qpF4ratio, which will be called using system

Usage

qpf4ratio_wrapper(
  pref,
  pops,
  bin = "~np29/o2bin/qpF4ratio",
  outdir = ".",
  parfile = NULL,
  blgsize = 0.05,
  fancyf4 = "YES",
  printonly = FALSE,
  env = "",
  verbose = TRUE
)

Arguments

pref	Path to and prefix of the packedancestrymap genotype files
pops	A vector of five populations, or a 5 x n matrix with population names. For each line alpha will be computed as ⁠f4(1,2; 3,4)/f4(1,2; 5,4)⁠
bin	Path to the qpF4ratio binary file
outdir	Output directory. files out, parfile, poplistname, popfilename may be overwritten
parfile	qpF4ratio parameter file. If this is specified, pops will be ignored.
blgsize	blgsize
fancyf4	fancyf4
printonly	Should the command be printed or executed?
env	Export environmental variables. See examples.
verbose	Print progress updates

Value

If printonly, the qpF4ratio command, otherwise a data frame with parsed qpF4ratio output

Examples

## Not run: 
pops = c('Denisova.DG', 'Altai_Neanderthal.DG', 'Vindija.DG', 'Chimp.REF', 'Mbuti.DG')
qpf4ratio_wrapper('genotype_prefix', pops, bin = 'path/to/qpDstat')

## End(Not run)

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