R: F-Statistics From Patterson et al

F4 {pegas} | R Documentation

## F-Statistics From Patterson et al

### Description

These functions compute the F-statistics developed by Patterson et al. (2012).

### Usage

    F2(x, allele.freq = NULL, population = NULL, check.data = TRUE,
       pops = NULL, jackknife.block.size = 10, B = 1e4)
    F3(x, allele.freq = NULL, population = NULL, check.data = TRUE,
       pops = NULL, jackknife.block.size = 10, B = 1e4)
    F4(x, allele.freq = NULL, population = NULL, check.data = TRUE,
       pops = NULL, jackknife.block.size = 10, B = 1e4)

### Arguments

`x` | an object of class `"loci"`.
`allele.freq` | alternatively, a list of allele (absolute) frequencies as output by `by.loci` (if this is used, `x` is ignored).
`population` | a column name or number giving which column of `x` should be treated as the population variable. By default, the column named “population” is used.
`check.data` | if `FALSE`, it is assumed that the user checked that all loci are strict SNPs. By default, the data are checked for the number of alleles and the non-SNP loci are dropped with a warning.
`pops` | a vector giving two, three, or four population names depending on the function. The order of these names is important (see Patterson et al. 2012). By default, the populations in `x` are taken in the order they appear, and an error is returned if the number of populations does not match the number required by the function.
`jackknife.block.size` | the size of the block used in the jackknife to assess the significance of the F-statistic (this should be around one thousandth of the number of loci, or not less than 10.
`B` | the number of replications of the bootstrap used to assess the significance of the F-statistic.

### Details

These functions are provisional versions.

It is much better to compute the allele frequencies, and then use `allele.freq` with different combinations of `pops`.

### Value

A vector with names.

### Author(s)

Emmanuel Paradis

### References

Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T. and Reich, D. (2012) Ancient admixture in human history. Genetics, 192, 1065–1093.

### See Also

`by.loci`, `Fst`, the package admixturegraph that can draw graphs from the output of this function.

[Package pegas version 1.1 Index]