Description | Installation | Usage
Package: PCAmatchR 0.3.3
Derek W. Brown
PCAmatchR: Match Cases to Controls Based on Genotype Principal Components
Matches cases to controls based on genotype principal components (PC). In order to produce better results, matches are based on the weighted distance of PCs where the weights are equal to the % variance explained by that PC. A weighted Mahalanobis distance metric (Kidd et al. (1987) <doi:10.1016/0031-3203(87)90066-5>) is used to determine matches.
Authors:
PCAmatchR_0.3.3.tar.gz
PCAmatchR_0.3.3.zip(r-4.7-any)PCAmatchR_0.3.3.zip(r-4.6-any)PCAmatchR_0.3.3.zip(r-4.5-any)
PCAmatchR_0.3.3.tgz(r-4.6-any)PCAmatchR_0.3.3.tgz(r-4.5-any)
PCAmatchR_0.3.3.tar.gz(r-4.7-any)PCAmatchR_0.3.3.tar.gz(r-4.6-any)
PCAmatchR_0.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PCAmatchR/json (API)
| # Install 'PCAmatchR' in R: |
| install.packages('PCAmatchR', repos = c('https://machiela-lab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/machiela-lab/pcamatchr/issues
Datasets:
- eigenvalues_1000G - First 20 eigenvalues of 2504 individuals from the 1000 Genome Project
- eigenvalues_all_1000G - All eigenvalues of 2504 individuals from the 1000 Genome Project
- PCs_1000G - First 20 principal components of 2504 individuals from the 1000 Genome Project
Last updated from:065900b045. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 137 | ||
| source / vignettes | OK | 202 | ||
| linux-release | OK | 129 | ||
| macos-release | OK | 134 | ||
| macos-oldrel | OK | 207 | ||
| windows-devel | OK | 87 | ||
| windows-release | OK | 79 | ||
| windows-oldrel | OK | 69 | ||
| wasm-release | OK | 95 |
Exports:match_makerplot_maker
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| First 20 eigenvalues of 2504 individuals from the 1000 Genome Project | eigenvalues_1000G |
| All eigenvalues of 2504 individuals from the 1000 Genome Project | eigenvalues_all_1000G |
| Weighted matching of controls to cases using PCA results. | match_maker |
| First 20 principal components of 2504 individuals from the 1000 Genome Project | PCs_1000G |
| Function to plot matches from match_maker output | plot_maker |