Package: pcadapt 4.4.2

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_4.4.2.tar.gz
pcadapt_4.4.2.zip(r-4.7-x86_64)pcadapt_4.4.2.zip(r-4.7-arm64)pcadapt_4.4.2.zip(r-4.6-x86_64)pcadapt_4.4.2.zip(r-4.6-arm64)pcadapt_4.4.2.zip(r-4.5-x86_64)
pcadapt_4.4.2.tgz(r-4.6-x86_64)pcadapt_4.4.2.tgz(r-4.6-arm64)pcadapt_4.4.2.tgz(r-4.5-x86_64)pcadapt_4.4.2.tgz(r-4.5-arm64)
pcadapt_4.4.2.tar.gz(r-4.7-arm64)pcadapt_4.4.2.tar.gz(r-4.7-x86_64)pcadapt_4.4.2.tar.gz(r-4.6-arm64)pcadapt_4.4.2.tar.gz(r-4.6-x86_64)
pcadapt_4.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pcadapt/json (API)

# 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

7.61 score 46 stars 444 scripts 814 downloads 64 mentions 14 exports 43 dependencies

Last updated from:01ed6ee6e4. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	159
linux-devel-x86_64	OK	188
source / vignettes	OK	222
linux-release-arm64	OK	147
linux-release-x86_64	OK	185
macos-release-arm64	OK	170
macos-release-x86_64	OK	535
macos-oldrel-arm64	OK	145
macos-oldrel-x86_64	OK	489
windows-devel-arm64	OK	404
windows-devel-x86_64	OK	176
windows-release-arm64	OK	424
windows-release-x86_64	OK	189
windows-oldrel-x86_64	OK	168
wasm-release	OK	140

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