Description Usage Arguments Format Details Examples
Given a allele_count
matrix, it computes the Fst statistic and its
bootstrap replications between all pairs of population using several
methods.
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fst(ac, method = fst_methods, snpwise = FALSE)
bootstrap_fst(
ac,
method = fst_methods,
boots = 100L,
block = 10L,
as_matrix = FALSE
)
|
ac |
allele count matrix for which to compute |
method |
fst estimator method. Using |
snpwise |
a boolean scalar idicating if should return a the statistic
for each variant (when |
boots |
number of bootstrap replicates to perform |
block |
statistic blocking size |
as_matrix |
if |
An object of class character
of length 5.
The estimator methods include Reich et al. (2019) (reich
),
Weir & Cockerham (1984) (weir_cockerham
or wc
), Hudson et al. (1992)
(hudson
) and Wright (1951) (wright
). These methods use different
approaches to estimate Fst. The Wright method is a biased estimator and
can be affected by different populations sizes, Hudson and Reich methods
are unbiased fast and tend to present reliable results on large variant
sizes, but limited precision snpwise. In other hand, Weir & Cockerham
method is the most common estimator (implemented by tools such as plink,
vcftools, and scikit-allele) and uses a population size correction to
reduce bias, but is a little slower than the other methods.
Please note that Reich method requires population sizes larger than 2 ( more than one diploid individual).
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