Wrapper function around the original qpF4ratio program

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

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

if (FALSE) {
pops = c('Denisova.DG', 'Altai_Neanderthal.DG', 'Vindija.DG', 'Chimp.REF', 'Mbuti.DG')
qpf4ratio_wrapper('genotype_prefix', pops, bin = 'path/to/qpDstat')
}