fs.dosage: Estimates F-statistics from dosage data

In jgx65/hierfstat: Estimation and Tests of Hierarchical F-Statistics

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 class 'fs.dosage'
plot(x, ...)

## S3 method for class '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))

Methods (by generic)

• plot(fs.dosage): Plot function for fs.dosage class

• print(fs.dosage): Print function for fs.dosage class

Author(s)

Jerome Goudet [e-mail]

Weir, BS and Goudet J. 2017 A Unified Characterization of Population Structure and Relatedness. Genetics (2017) 206:2085

See Also

betas

Examples

## 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)))

## End(Not run)

jgx65/hierfstat documentation built on April 20, 2023, 8:34 a.m.