Description
Usage
Arguments
Value
References
Examples
View source: R/qpdstat.R
Computes f2 statistics from f2 blocks of the form f2(A, B)
 (
,
pop1 = ,
pop2 = ,
boot = ,
sure = ,
unique_only = ,
verbose =
)

data 
Input data in one of three forms:
A 3d array of blocked f2 statistics, output of f2_from_precomp or extract_f2 (fastest option)
A directory which contains precomputed f2statistics
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), each block will be left out at a time and the covariance matrix
of the f statistics will be computed using blockjackknife. Otherwise bootstrap resampling is performed n times,
where n is either equal to boot if it is an integer, or equal to the number of blocks if boot is TRUE .
The the covariance matrix of the f statistics will be computed using bootstrapping.

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

f2
returns a data frame with f2 statistics
Patterson, N. et al. (2012) Ancient admixture in human history Genetics
Peter, B. (2016) Admixture, Population Structure, and FStatistics Genetics
 pop1 = 'Denisova.DG'
pop2 = ('Altai_Neanderthal.DG', 'Vindija.DG')
(, pop1, pop2)
## Not run:
(f2_dir, pop1, pop2)
## End(Not run)

uqrmaie1/admixtools documentation built on Sept. 16, 2020, 5:55 a.m.