F4: 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)

Value

A vector with names.

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.

Author

Emmanuel Paradis

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.

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.