Estimate f4 differences

Source: R/qpdstat.R

Estimate f4 differences

qpf4diff(data, pops, boot = FALSE, verbose = FALSE)

Arguments

data

Input data in one of three forms:

  1. A 3d array of blocked f2 statistics, output of f2_from_precomp or f2_from_geno (fastest option)

  2. A directory which contains pre-computed f2-statistics

  3. The prefix of genotype files (slowest option)

pops

A vector of 5 populations or a five column population matrix. The following ratios will be computed: f4(1, 2; 3, 4)/f4(1, 2; 5, 4)

boot

If FALSE (the default), block-jackknife resampling will be used to compute standard errors. Otherwise, block-bootstrap resampling will be used to compute standard errors. If boot is an integer, that number will specify the number of bootstrap resamplings. If boot = TRUE, the number of bootstrap resamplings will be equal to the number of SNP blocks.

verbose

Print progress updates

Value

qpf4diff returns a data frame with f4 ratios