compute.f4ratio: Compute F4ratio (estimation of admixture rate) from an fstats object

Description

Compute F4ratio (estimation of admixture rate) from an fstats object

Usage

compute.f4ratio(x, num.quadruplet, den.quadruplet)

Value

Either a scalar corresponding to the estimated admixture rate or, if F2 block-jackknife samples are available in the input fstats object (i.e., compute.fstats was run with return.F2.blockjackknife.samples = TRUE) a vector with three elements corresponding to the estimate of the admixture rate, the block-jacknife mean (may be slightly different than the previous since not exactly the same set of markers are used) and the standard error of the estimates.

Arguments

x: A fstats object containing estimates of fstats
num.quadruplet: A character vector for the F4 quadruplet used in the F4ratio numerator (should be of the form "A,O;C,X" where A, O, C and X are the names of the population as defined in the countdata or pooldata object used to obtain fstats, see details)
den.quadruplet: A character vector for the F4 quadruplet used in the F4ratio denominator (should be of the form "A,O;C,B" where A, O, C and B are the names of the populations as defined in the countdata or pooldata object used to obtain fstats, see details))

Details

Assuming a 4 population phylogeny rooted with an outgroup O of the form (((A,B);C);O) and an admixed population X with two source populations related to B and C, the admixture rate alpha of the B-related ancestry is obtained using the ratio F4(A,O;C,X)/F4(A,O;C,B) (see Patterson et al., 2012 for more details).

Examples

Run this code

 make.example.files(writing.dir=tempdir())
 pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15))
 res.fstats=compute.fstats(pooldata)