F4  R Documentation 
These functions compute the Fstatistics developed by Patterson et al. (2012).
F2(x, allele.freq = NULL, population = NULL, check.data = TRUE, pops = NULL, jackknife.block.size = 10, B = 1e4) F3(x, allele.freq = NULL, population = NULL, check.data = TRUE, pops = NULL, jackknife.block.size = 10, B = 1e4) F4(x, allele.freq = NULL, population = NULL, check.data = TRUE, pops = NULL, jackknife.block.size = 10, B = 1e4)
x 
an object of class 
allele.freq 
alternatively, a list of allele (absolute)
frequencies as output by 
population 
a column name or number giving which column of

check.data 
if 
pops 
a vector giving two, three, or four population names
depending on the function. The order of these names is important
(see Patterson et al. 2012). By default, the populations in

jackknife.block.size 
the size of the block used in the jackknife to assess the significance of the Fstatistic (this should be around one thousandth of the number of loci, or not less than 10. 
B 
the number of replications of the bootstrap used to assess the significance of the Fstatistic. 
These functions are provisional versions.
It is much better to compute the allele frequencies, and then use
allele.freq
with different combinations of pops
.
A vector with names.
Emmanuel Paradis
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T. and Reich, D. (2012) Ancient admixture in human history. Genetics, 192, 1065–1093.
by.loci
, Fst
, the package
admixturegraph that can draw graphs from the output of this
function.
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