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

In admixr: An Interface for Running 'ADMIXTOOLS' Analyses

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)

Arguments

data	EIGENSTRAT data object.
outdir	Where to put all generated files (temporary directory by default).
params	Named list of parameters and their values.
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.

Value

Data frame object with calculated statistics

Examples

## Not run: # 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
)

## End(Not run)

admixr documentation built on July 8, 2020, 6:19 p.m.