README.md

In MaikeMorrison/FSTruct: Measure variability in population structure estimates

FSTruct – Measure variability in population structure estimates

The FSTruct R package provides an Fst-based tool to compare the variability of Q matrices (matrices with rows of ancestry coefficients, the default output of population structure inference programs such a STRUCTURE and ADMIXTURE).

The package includes four functions:

• Q_stat calculates Fst/Fst^max (a normalized measure of variability) for a Q matrix.
• Q_bootstrap generates bootstrap replicates of one or more Q matrices along with associated statistics, including Fst/Fst^max, as well as statistical tests to compare bootstrap distributions of Fst/Fst^max .
• Q_plot plots Q matrices using ggplot2.
• Q_simulate generates one or more Q matrices using the Dirichlet distribution.

This package accompanies the paper “FSTruct: an FST-based tool for measuring ancestry variation in inference of population structure” by Maike Morrison, Nicolas Alcala, and Noah Rosenberg. You can access the paper in Molecular Ecology Resources at this link. Q matrix files for data examples that appeared in this paper are available on this GitHub repository, as well.

Installation

You can install this package from GitHub with the following R code:

# install.packages("devtools")
devtools::install_github("MaikeMorrison/FSTruct")

If you have not used R before: Install R (not optional) and RStudio (optional). In the R or RStudio console, paste install.packages("devtools") and hit enter to run. Next run devtools::install_github("MaikeMorrison/FSTruct", dependenceies = TRUE) to install FSTruct. Then see the introductory vignette for details on how to use this package.

Usage

For a step-by-step guide to this package, read the introductory vignette.

For details on the functions and their usage, read the FSTruct manual.

MaikeMorrison/FSTruct documentation built on Aug. 26, 2023, 7:01 a.m.