Package: pcadapt 4.4.0
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:
pcadapt_4.4.0.tar.gz
pcadapt_4.4.0.zip(r-4.5)pcadapt_4.4.0.zip(r-4.4)pcadapt_4.4.0.zip(r-4.3)
pcadapt_4.4.0.tgz(r-4.4-x86_64)pcadapt_4.4.0.tgz(r-4.4-arm64)pcadapt_4.4.0.tgz(r-4.3-x86_64)pcadapt_4.4.0.tgz(r-4.3-arm64)
pcadapt_4.4.0.tar.gz(r-4.5-noble)pcadapt_4.4.0.tar.gz(r-4.4-noble)
pcadapt_4.4.0.tgz(r-4.4-emscripten)pcadapt_4.4.0.tgz(r-4.3-emscripten)
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
Last updated 2 months agofrom:792610704b. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 02 2024 |
R-4.5-win-x86_64 | OK | Nov 02 2024 |
R-4.5-linux-x86_64 | OK | Nov 02 2024 |
R-4.4-win-x86_64 | OK | Nov 02 2024 |
R-4.4-mac-x86_64 | OK | Nov 02 2024 |
R-4.4-mac-aarch64 | OK | Nov 02 2024 |
R-4.3-win-x86_64 | OK | Nov 02 2024 |
R-4.3-mac-x86_64 | OK | Nov 02 2024 |
R-4.3-mac-aarch64 | OK | Nov 02 2024 |
Exports:bed2matrixget.pcget.pop.namesget.score.colorhist_plotmanhattan_plotpcadaptqq_plotread.pcadaptrun.pcadaptscore_plotscree_plotvcf2pcadaptwriteBed
Dependencies:BHbigassertrbigparallelrbigutilsrbitclicodetoolscolorspacedata.tableDEoptimRdoParallelfansifarverffflockforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmmapcharrmunsellnabornlmeparallellypillarpkgconfigR6RColorBrewerRcppRcppEigenRhpcBLASctlrlangrmiorobustbaseRSpectrascalestibbleutf8vctrsviridisLitewithr
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 |