Package: pcadapt 4.4.1

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_4.4.1.tar.gz
pcadapt_4.4.1.zip(r-4.7)pcadapt_4.4.1.zip(r-4.6)pcadapt_4.4.1.zip(r-4.5)
pcadapt_4.4.1.tgz(r-4.6-x86_64)pcadapt_4.4.1.tgz(r-4.6-arm64)pcadapt_4.4.1.tgz(r-4.5-x86_64)pcadapt_4.4.1.tgz(r-4.5-arm64)
pcadapt_4.4.1.tar.gz(r-4.7-arm64)pcadapt_4.4.1.tar.gz(r-4.7-x86_64)pcadapt_4.4.1.tar.gz(r-4.6-arm64)pcadapt_4.4.1.tar.gz(r-4.6-x86_64)
pcadapt_4.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

7.45 score 45 stars 422 scripts 762 downloads 64 mentions 14 exports 43 dependencies

Last updated from:328a46d384. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	180
linux-devel-x86_64	OK	186
source / vignettes	OK	228
linux-release-arm64	OK	176
linux-release-x86_64	OK	174
macos-release-arm64	OK	149
macos-release-x86_64	OK	283
macos-oldrel-arm64	OK	155
macos-oldrel-x86_64	OK	497
windows-devel	OK	176
windows-release	OK	185
windows-oldrel	OK	218
wasm-release	OK	166

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 cpp11 data.table DEoptimR doParallel farver ff flock foreach ggplot2 glue gtable isoband iterators labeling lattice lifecycle magrittr Matrix mmapcharr nabor parallelly R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RhpcBLASctl rlang rmio robustbase RSpectra S7 scales 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