admixr (version 0.9.2)

f4ratio: Calculate the D, f4, f4-ratio, or f3 statistic.

Description

Calculate the D, f4, f4-ratio, or f3 statistic.

Usage

f4ratio(data, X, A, B, C, O, outdir = NULL, params = NULL)
d(
  data,
  W,
  X,
  Y,
  Z,
  quartets = NULL,
  outdir = NULL,
  f4mode = FALSE,
  params = NULL
)
f4(data, W, X, Y, Z, quartets = NULL, outdir = NULL, params = NULL)
f3(data, A, B, C, outdir = NULL, inbreed = FALSE, params = NULL)

Value

Data frame object with calculated statistics

Arguments

data

EIGENSTRAT data object.

outdir

Where to put all generated files (temporary directory by default).

params

Named list of parameters and their values. For instance, params = list(allsnps = "YES") or params = list(blgsize = 0.01) (or an arbitrary combination of parameters using a list with multiple named elements).

W, X, Y, Z, A, B, C, O

Population names according to the nomenclature used in Patterson et al., 2012.

quartets

List of character vectors (quartets of population/sample labels)

f4mode

Calculate the f4 statistic instead of the D statistic.

inbreed

See README.3PopTest in ADMIXTOOLS for an explanation.

Examples

if (FALSE) # download an example genomic data set and prepare it for analysis
snps <- eigenstrat(download_data(dirname = tempdir()))

# define a set of populations to analyze
pops <- c("French", "Sardinian", "Han", "Papuan", "Dinka")

result_f4ratio <- f4ratio(
    X = pops, A = "Altai", B = "Vindija", C = "Yoruba", O = "Chimp",
    data = snps
)

result_d <- d(
    W = pops, X = "Yoruba", Y = "Vindija", Z = "Chimp",
    data = snps
)

result_f4 <- f4(
    W = pops, X = "Yoruba", Y = "Vindija", Z = "Chimp",
    data = snps
)

result_f3 <- f3(
    A = pops, B = "Mbuti", C = "Khomani_San",
    data = snps
)