f2: Estimate f2 statistics

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Estimate f2 statistics

Description

Computes f2 statistics from f2 blocks of the form f2(A, B)

Usage

f2(
  data,
  pop1 = NULL,
  pop2 = NULL,
  boot = FALSE,
  sure = FALSE,
  unique_only = TRUE,
  verbose = FALSE,
  ...
)

Arguments

data	Input data in one of three forms: A 3d array of blocked f2 statistics, output of f2_from_precomp or f2_from_geno (fastest option) A directory which contains pre-computed f2-statistics The prefix of genotype files (slowest option)
pop1	One of the following four: NULL: all possible population combinations will be returned A vector of population labels. All combinations with the other pop arguments will be returned A matrix with population combinations to be tested, with one population per column and one combination per row. Other pop arguments will be ignored. the location of a file (poplistname or popfilename) which specifies the populations or population combinations to be tested. Other pop arguments will be ignored.
pop2	A vector of population labels
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.
sure	The number of population combinations can get very large. This is a safety option that stops you from accidently computing all combinations if that number is large.
unique_only	If TRUE (the default), redundant combinations will be excluded
verbose	Print progress updates
...	Additional arguments passed to f2_from_geno when data is a genotype prefix

Value

f2 returns a data frame with f2 statistics

References

Patterson, N. et al. (2012) Ancient admixture in human history Genetics

Peter, B. (2016) Admixture, Population Structure, and F-Statistics Genetics

Examples

pop1 = 'Denisova.DG'
pop2 = c('Altai_Neanderthal.DG', 'Vindija.DG')
f2(example_f2_blocks, pop1, pop2)
## Not run: 
f2(f2_dir, pop1, pop2)

## End(Not run)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.