# 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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17``` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27``` ```## 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.