Fast Principal Component Analysis for Outlier Detection

Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) .


pcadapt has been developed to detect genetic markers involved in biological adaptation. pcadapt provides statistical tools for outlier detection based on Principal Component Analysis (PCA).

To run the package, you can install it from CRAN:

install.packages("pcadapt")
library(pcadapt)

A tutorial for pcadapt is available. To access to the vignette, type the following command in your R console:

browseVignettes("pcadapt")

If you desire to install from GitHub, run the following commands:

install.packages("devtools")
devtools::install_github("BioShock38/pcadapt")

Reference

Luu, Keurcien, Eric Bazin, and Michael GB Blum. "pcadapt: an R package to perform genome scans for selection based on principal component analysis." bioRxiv (2016): 056135.

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Reference manual

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install.packages("pcadapt")

4.0.1 by Michael Blum, 2 months ago


Browse source code at https://github.com/cran/pcadapt


Authors: Keurcien Luu [aut], Michael Blum [aut, cre], Florian Privé [aut], Eric Bazin [ctb], Nicolas Duforet-Frebourg [ctb]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports data.table, ggplot2, magrittr, mmapcharr, plotly, Rcpp, robust, RSpectra, vcfR

Suggests knitr, rmarkdown, testthat, shiny

Linking to Rcpp, BH, mmapcharr


See at CRAN