Description Usage Arguments Details Value
Takes allele frequency data from one site only and calculates Wright's fixation index (Fst).
1 2 3 4 5 6 7 8 | site_fst(
freq,
support,
info,
map,
support_thres = 1,
method = "Weir-Cockerham"
)
|
freq |
A 1 x (n+1) tibble. One of the columns must correspond to 'site_id', and the rest of the columns correspond to one sample each. Entries under each sample correspond to allele frequencies. |
support |
A 1 x (n+1) tibble. Columns must match columns in freq. Values must be numeric and indicate support of each allele frequencuy |
info |
A tiblle with one row. One column must correspond to 'site_id'. The rest of the columns contain information about the site |
map |
A tibble with columns 'sample' (corresponding to column names) in freq and support, and 'Group' corresponding to the populations used for Fst calculations. |
support_thres |
Minimum value in support tibble to keep a sample for this site |
method |
The method to calculate Fst. Currently only the 'Weir-Cockerham' method from 1984, and the 'Fstpool' methods are implemented. |
It works only for haploid individuals (e.g proportion of heterozygous is 0).
A tibble
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