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EGT3C-2019

Instructor: Angela P. Fuentes-Pardo, PhD, Uppsala University, e-mail: apfuentesp@gmail.com

2019-11-19

Objectives

  • Become familiarized with R
  • Learn how to perform population genomics analysis in R

Table of contents

  1. Basic statistics

    • Genetic diversity (Ho, He) - R
  2. Population genetic structure

    • Pairwise FST - R
    • Unsupervised clustering (PCA, nMDS) - R
    • Model-based clustering - ADMIXTURE
    • Genotype x Environment Association (Redundancy Analysis, RDA) - R

Programs and R packages required

install.packages(c("ade4", "adegenet", "ape", "circlize", "ComplexHeatmap", "data.table", "devtools", "diveRsity", "dplyr", "gdistance", "genepopedit", "geosphere", "ggplot2", "ggpubr", "ggrepel", "ggsn", "gplots", "hierfstat", "igraph", "knitr", "lattice", "magrittr", "mapdata", "maps", "maptools", "marmap", "mmod", "pcadapt", "pegas", "pegas", "phangorn", "pinfsc50", "plyr", "poolfstat", "poppr", "psych", "qqman", "randomForest", "RColorBrewer", "RCurl", "reshape2", "rgdal", "rgeos", "rmatio", "Rmisc", "sp", "stringr", "tidyr", "tidyverse", "tools", "treemap", "vcfR", "vegan", "VennDiagram", "viridisLite"), repos = "http://cran.rstudio.com", dependencies = TRUE)

# If genepopedit is not available, install it.
if (!require("genepopedit")) {
  if (!require("devtools")) install.packages("devtools") # Install the R package devtools
  devtools::install_github("rystanley/genepopedit") # Install the package from *Github*
}

Note: You need to have java JDK v1.8 and python3 previously installed in your machine. If you are having problems installing some R packages (e.g. devtools), search in the internet for a solution. Hint: A system library might be missing in your machine.

Data

  • SNP genotype data (96 loci) of 1308 individuals from 27 locations (Lehnert et al.,2017). SNP panel of 96 SNPs generated from RAD-seq data of Wyngaarden et al. (2017)
  • Environmental data of sampling locations

Activities

Go to the Wiki page at the top of the repository, and follow the menu on the right to go over all the proposed exercises in R.

References and other recommended readings:

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