README.md

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

Overview

Capturing uncertainty in genetic population assignment is one of the key advantages of using Bayesian inference through programs such as STRUCTURE. However, this uncertainty is often ignored when using assignment inferences in downstream analysis, such as in landscape genetics.

The STUCTURE.popgen package overcomes these limitations by providing functions for using supplied q-matrix assignment probabilities to account for uncertainty while calculating population genetics metrics among inferred clusters. Functions are also provided for working more seamlessly through well-established R packages (adegenet, PopGenReport, and hierfstat) to calculate individual-based and population-based population genetics metrics.

Installation

You can install STUCTURE.popgen from GitHub with:

# install.packages("devtools")
devtools::install_github("nicholasjclark/STRUCTURE.popgen")

Brief Introduction to Current Functions

The STRUCTURE.popgen function is the workhorse of the package. This function randomly assigns individuals to pre-identified population clusters using STRUCTURE assignment probabilities, which are provided in a supplied q-matrix (Pritchard et al. 2000).

A range of wrapper functions are also provided to calculate various commonly-used population genetics statistics. For example, the fis.STRUCTURE.popgen function assigns individuals to clusters using STRUCTURE assignment probabilities provided in the qmatrix, calculates individual Fis values and compares cluster-level Fis values using an analysis of variance (ANOVA). This can be repeated many times (using the nreps argument) to calculate summary statistics (i.e. confidence intervals) by allowing for uncertainty in individual assignment probabilities. Other functions are currently provided to calculate Fst, allelic richness and inbreeding probabilities.

This package is currently under development, so watch this space to keep track of improved functionality and flexibility.

References

Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.

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