Calculate the D, f4, f4-ratio, or f3 statistic.
Calculate the D, f4, f4-ratio, or f3 statistic.
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)
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. |
Data frame object with calculated statistics
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.