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) .


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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("bcm-uga/pcadapt")

Reference

[1] Luu, K., Bazin, E., & Blum, M. G. (2017). pcadapt: an R package to perform genome scans for selection based on principal component analysis. Molecular Ecology Resources, 17(1), 67-77.

[2] Duforet-Frebourg, N., Luu, K., Laval, G., Bazin, E., & Blum, M. G. (2015). Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Molecular biology and evolution, msv334.

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Reference manual

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install.packages("pcadapt")

4.3.3 by Florian Privé, 6 months ago


https://github.com/bcm-uga/pcadapt


Report a bug at https://github.com/bcm-uga/pcadapt/issues


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


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


Documentation:   PDF Manual  


GPL (>= 2) license


Imports bigutilsr, data.table, ggplot2, magrittr, mmapcharr, Rcpp, RSpectra

Suggests plotly, shiny, spelling, testthat, vcfR

Linking to mmapcharr, Rcpp, rmio


Suggested by bigsnpr.


See at CRAN