Instructor: Angela P. Fuentes-Pardo, PhD, Uppsala University, e-mail: apfuentesp@gmail.com
- Become familiarized with R
- Learn how to perform population genomics analysis in R
-
Basic statistics
- Genetic diversity (Ho, He) -
R
- Genetic diversity (Ho, He) -
-
Population genetic structure
- Pairwise FST -
R
- Unsupervised clustering (PCA, nMDS) -
R
- Model-based clustering -
ADMIXTURE
- Genotype x Environment Association (Redundancy Analysis, RDA) -
R
- Pairwise FST -
- plink v1.9
- PGDSpider
- Admixture
- R
- Rstudio
- R packages:
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.
- 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
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.
- Special issue in Molecular Ecology on Population Genomics in R
- Lehnert et al. (2019) Fine-scale temperature-associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus). Heredity 122:69–80
- Wyngaarden et al. (2017) Identifying patterns of dispersal, connectivity and selection in the sea scallop, Placopecten magellanicus, using RADseq-derived SNPs. Evolutionary Applications 10:102–117