R package {pcadapt} was developed to detect genetic markers involved in biological adaptation. This package uses statistical tools for outlier detection based on Principal Component Analysis (PCA).
A tutorial for {pcadapt} is available on pcadapt’s website.
News: Our paper describing version 4 of pcadapt (which has been available for quite some time now) is out. Please cite the newest paper (see Refs below).
# From CRAN
install.packages("pcadapt")
# From GitHub
remotes::install_github("bcm-uga/pcadapt")Privé, F., Luu, K., Vilhjálmsson, B. J., & Blum, M. G.B. (2020). Performing highly efficient genome scans for local adaptation with R package pcadapt version 4. Molecular Biology and Evolution 37.7 (2020): 2153–2154.
Luu, K., Bazin, E., & Blum, M. G.B. (2017). pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular Ecology Resources, 17(1), 67–77.
Duforet-Frebourg, N., Luu, K., Laval, G., Bazin, E., & Blum, M. G.B. (2015). Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Molecular biology and evolution, 33(4), 1082–1093.