fs.dosage: Estimates F-statistics from dosage data
Description
Reports individual inbreeding coefficients, Population specific and pairwise Fsts, and Fiss from dosage data
Usage
fs.dosage(dos, pop, matching = FALSE)
# S3 method for fs.dosage
plot(x, ...)
# S3 method for fs.dosage
print(x, digits = 4, ...)
fst.dosage(dos, pop, matching = FALSE)
fis.dosage(dos, pop, matching = FALSE)
pairwise.fst.dosage(dos, pop, matching = FALSE)
Arguments
dos
either a matrix with snps columns and individuals in rows containing allelic dosage (number [0,1 or 2] of alternate alleles);
or a square matrix with as many rows and columns as the number of individuals and containing the proportion of matching alleles
pop
a vector containing the identifier of the population to which the individual in the corresponding row belongs
matching
logical:TRUE if dos is a square matrix of allelic matching; FALSE otherwise
x
a fs.dosage object
...
further arguments to pass
digits
number of digits to print
Value
Fi list of individual inbreeding coefficients, estimated with the reference being the population to which the individual belongs.
FsM matrix containing population specific FSTs on the diagonal. The off diagonal elements contains the average of the kinships
for pairs of individuals, one from each population, relative to the mean kinship for pairs of individuals between populations.
Fst2x2 matrix containing pairwise FSTs
Fs The first row contains population specific and overall Fis, the second row population specific
(average \(\hat{\beta_{ST}^i}\) over loci) FSTs and overall Fst \(\hat{\beta_{ST}}\) (see Table 3 of
Weir and Goudet, 2017 (Genetics))
# NOT RUN { dos<-matrix(sample(0:2,size=10000,replace=TRUE),ncol=100)
fs.dosage(dos,pop=rep(1:5,each=20))
plot(fs.dosage(dos,pop=rep(1:5,each=20)))
# }# NOT RUN {# }