qpdstat_wrapper: Wrapper function around the original qpDstat program

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Wrapper function around the original qpDstat program

Description

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

Usage

qpdstat_wrapper(
  pref,
  pop1,
  pop2 = NULL,
  pop3 = NULL,
  pop4 = NULL,
  bin = "~np29/o2bin/qpDstat",
  outdir = ".",
  parfile = NULL,
  f4mode = "YES",
  inbreed = "NO",
  printonly = FALSE,
  env = "",
  verbose = TRUE
)

Arguments

pref	Path to and prefix of the packedancestrymap genotype files
pop1	One of the following four: NULL: populations will be read from poplistname or popfilename specified in parfile A vector of population labels A data frame in which the first four columns specify the population combinations to be tested. pop2, pop3, pop4 will be ignored. the location of a file (poplistname or popfilename) which specifies the populations or population combinations to be tested. pop2, pop3, pop4 will be ignored.
pop2	A vector of population labels
pop3	A vector of population labels
pop4	A vector of population labels
bin	Path to the qpDstat binary file
outdir	Output directory. files out, parfile, poplistname, popfilename may be overwritten
parfile	qpDstat parameter file. If this is specified, pop, pop2, pop3, and pop4 will be ignored.
f4mode	f4mode
inbreed	inbreed
printonly	Should the command be printed or executed?
env	Export environmental variables. See examples.
verbose	Print progress updates

Value

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

Examples

## Not run: 
pop1 = 'Denisova.DG'
pop2 = c('Altai_Neanderthal.DG', 'Vindija.DG')
pop3 = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG')
pop4 = 'Switzerland_Bichon.SG'
qpdstat_wrapper('genotype_prefix', pop1, pop2, pop3, pop4,
  bin = 'path/to/qpDstat', pref = 'path/to/packedancestrymap_prefix')

## End(Not run)

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