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