inbreed.STRUCTURE.popgen: Subsample SNPs and estimate individual inbreeding...

In nicholasjclark/STRUCTURE.popgen: Population genetics calculations using STRUCTURE assignment probabilities

Description

This function assigns individuals to known (i.e. provided) populations or to clusters using STRUCTURE assignment probabilities provided in the qmatrix. It then calculates inbreeding coefficients for individuals and compares cluster-level inbreeding with an ANOVA.

Usage

inbreed.STRUCTURE.popgen(allele.dat, qmatrix.prob, samp.snps, nreps, ncores,
  nsamp, NA.symbol, qmatrix = NULL, ind.populations = NULL,
  nclusters = NULL)

Arguments

allele.dat	Dataframe/matrix containing '/' separated allele data, with rownames representing individuals
qmatrix.prob	(optional) Logical. If TRUE, a supplied STRUCTURE qmatrix will be used to randomly assign individuals to clusters based on assignment probabilities. Default is FALSE
samp.snps	Logical. If TRUE, a specified number of SNPs will be randomly sampled in each iteration to account for uncertainty and speed computations. Default is FALSE
nreps	Integer. The number of times to repeat the subsampling and estimate inbreeding. Default is 100
ncores	(optional) Integer. The number of cores to split job across. Default is 1 (no parallelisation)
nsamp	(optional) Integer. The number of SNPs to sample during each iteration
NA.symbol	The code used to represent missing allele data
qmatrix	(optional) The STRUCTURE qmatrix, with individuals in column 'ind'. To be used if qmatrix.prob = TRUE
ind.populations	(optional) Matrix. Population assignments for individuals, with rownames representing individuals
nclusters	(optional) Integer. The number of clusters identified by STRUCTURE

Value

A list of two elements:

lin.coefs: Tukey's population comparisons from repeated ANOVAs comparing individual inbreeding estimates across populations.

raw.vals: summaries of the raw inbreeding estimates for each individual

nicholasjclark/STRUCTURE.popgen documentation built on May 25, 2019, 10:38 p.m.