Package: pcadapt 4.4.0

Florian Privé

pcadapt: 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) <doi:10.1111/1755-0998.12592> and later revised in (Privé, 2020) <doi:10.1093/molbev/msaa053>.

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

pcadapt_4.4.0.tar.gz
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pcadapt.pdf |pcadapt.html✨
pcadapt/json (API)
NEWS

# Install 'pcadapt' in R:

install.packages('pcadapt', repos = c('https://bcm-uga.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bcm-uga/pcadapt/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

7.68 score 40 stars 327 scripts 1.2k downloads 64 mentions 14 exports 50 dependencies

Last updated 6 months agofrom:792610704b. Checks:11 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 02 2025
R-4.5-win-x86_64	OK	Mar 02 2025
R-4.5-mac-x86_64	OK	Mar 02 2025
R-4.5-mac-aarch64	OK	Mar 02 2025
R-4.5-linux-x86_64	OK	Mar 02 2025
R-4.4-win-x86_64	OK	Mar 02 2025
R-4.4-mac-x86_64	OK	Mar 02 2025
R-4.4-mac-aarch64	OK	Mar 02 2025
R-4.3-win-x86_64	OK	Mar 02 2025
R-4.3-mac-x86_64	OK	Mar 02 2025
R-4.3-mac-aarch64	OK	Mar 02 2025

Exports:bed2matrix get.pc get.pop.names get.score.color hist_plot manhattan_plot pcadapt qq_plot read.pcadapt run.pcadapt score_plot scree_plot vcf2pcadapt writeBed

Dependencies:BH bigassertr bigparallelr bigutilsr bit cli codetools colorspace data.table DEoptimR doParallel fansi farver ff flock foreach ggplot2 glue gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv mmapcharr munsell nabor nlme parallelly pillar pkgconfig R6 RColorBrewer Rcpp RcppEigen RhpcBLASctl rlang rmio robustbase RSpectra scales tibble utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert a bed to a matrix	bed2matrix
Get the principal component the most associated with a genetic marker	get.pc
Principal Component Analysis for outlier detection	pcadapt pcadapt.pcadapt_bed pcadapt.pcadapt_matrix pcadapt.pcadapt_pool
pcadapt visualization tool	plot.pcadapt
File Converter	read.pcadapt
Shiny app	run.pcadapt
Write PLINK files	writeBed