qp3pop_wrapper: Wrapper function around the original qp3Pop program

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Wrapper function around the original qp3Pop program

Description

Computes f3 statistics of the form f3(A; B, C). Equivalent to (f2(A, B) + f2(A, C) - f2(B, C)) / 2 and to f4(A, B; A, C). Requires a working installation of qp3Pop, which will be called using system

Usage

qp3pop_wrapper(
  pref,
  source1,
  source2 = NULL,
  target = NULL,
  bin = "~np29/o2bin/qp3Pop",
  outdir = ".",
  parfile = NULL,
  inbreed = "NO",
  outgroupmode = "NO",
  printonly = FALSE,
  env = "",
  verbose = TRUE
)

Arguments

pref	Path to and prefix of the packedancestrymap genotype files
source1	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 triples to be tested. source2, target will be ignored. The location of a file (poplistname or popfilename) which specifies the populations or population combinations to be tested. source2 and target will be ignored.
source2	A vector of population labels
target	A vector of population labels
bin	Path to the qp3Pop binary file
outdir	Output directory. files out, parfile, poplistname, popfilename may be overwritten
parfile	qp3Pop parameter file. If this is specified, source1, source2, target will be ignored.
inbreed	inbreed
outgroupmode	outgroupmode
printonly	Should the command be printed or executed?
env	Export environmental variables. See examples.
verbose	Print progress updates

Value

If printonly, the qp3Pop command, otherwise a data frame with parsed qp3Pop output

Examples

## Not run: 
source1 = c('Altai_Neanderthal.DG', 'Vindija.DG')
source2 = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG')
target = 'Denisova.DG'
qp3pop_wrapper('genotype_prefix', source1, source2, target,
  bin = 'path/to/qp3Pop')

## End(Not run)

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