Estimate admixture proportions via f4 ratios

Source: R/qpdstat.R

Estimate admixture proportions via f4 ratios

qpf4ratio(
  data,
  pops,
  auto_only = TRUE,
  blgsize = 0.05,
  poly_only = FALSE,
  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)

auto_only

Use only chromosomes 1 to 22.

blgsize

SNP block size in Morgan. Default is 0.05 (5 cM). If blgsize is 100 or greater, if will be interpreted as base pair distance rather than centimorgan distance.

poly_only

Exclude sites with identical allele frequencies in all populations.

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

qpf4ratio returns a data frame with f4 ratios