qp3pop: Estimate f3 statistics

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Estimate f3 statistics

Description

Computes f3 statistics of the form f3(A; B, C). When using the same SNPs for all populations, this is equivalent to (f2(A, B) + f2(A, C) - f2(B, C)) / 2 and to f4(A, B; A, C)

Usage

qp3pop(
  data,
  pop1 = NULL,
  pop2 = NULL,
  pop3 = NULL,
  boot = FALSE,
  sure = FALSE,
  unique_only = TRUE,
  blgsize = NULL,
  block_lengths = NULL,
  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
pop3	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 f3blockdat_from_geno if data is a genotype prefix, or to get_f2 otherwise

Details

There are several arguments that can be passed via ... which affect the estimated f3-statistics. The default options are the same as in the original qp3pop program, but some options are not effective when using precomputed f2-statistics. See examples for more information.

Value

qp3pop returns a data frame with f3 statistics

Alias

f3

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')
pop3 = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG')
qp3pop(example_f2_blocks, pop1, pop2, pop3)

pops = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG')
qp3pop(example_f2_blocks, pops)
qp3pop(example_f2_blocks, pops, unique_only = FALSE)
## Not run: 
qp3pop(f2_dir, pop1, pop2, pop3)

Below are three scenarios, and in each one `qp3pop()` and `qp3pop_wrapper()`
should give the same or very similar estimates. Note that to compute `f3(A; B, C)`,
`qp3pop_wrapper()` expects the populations to be in the order `B`, `C`, `A`.

prefix = '/path/to/geno/prefix'
qp3popbin = '/path/to/AdmixTools/bin/qp3Pop'
pops = dimnames(example_f2_blocks)[[1]]
qp3pop_wrapper(prefix, pops[2], pops[3], pops[1], bin = qp3popbin, outgroupmode = FALSE)
qp3pop(prefix, pops[1], pops[2], pops[3])
qp3pop(prefix, pops[1], pops[2], pops[3], poly_only = TRUE)
qp3pop_wrapper(prefix, pops[2], pops[3], pops[1], bin = qp3popbin, outgroupmode = TRUE)
qp3pop(prefix, pops[1], pops[2], pops[3], outgroupmode = TRUE)
f2b = f2_from_geno(prefix, pops = pops[1:3], poly_only = FALSE)
qp3pop(f2b, pops[1], pops[2], pops[3])
qp3pop_wrapper(prefix, pops[1], pops[3], pops[2], bin = qp3popbin, outgroupmode = TRUE)
qp3pop(prefix, pops[2], pops[1], pops[3], outgroupmode = TRUE, apply_corr = FALSE)

## End(Not run)

uqrmaie1/admixtools documentation built on March 20, 2024, 8:24 a.m.