Introduction | Sample usage | lfa | af | Data Input | References
Package: lfa 2.13.0
Alejandro Ochoa
lfa: Logistic Factor Analysis for Categorical Data
Logistic Factor Analysis is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter. The main method estimates genetic population structure from genotype data. There are also methods for estimating individual-specific allele frequencies using the population structure. Lastly, a structured Hardy-Weinberg equilibrium (HWE) test is developed, which quantifies the goodness of fit of the genotype data to the estimated population structure, via the estimated individual-specific allele frequencies (all of which generalizes traditional HWE tests).
Authors:
lfa_2.13.0.tar.gz
lfa_2.13.0.zip(r-4.7)lfa_2.13.0.zip(r-4.6)lfa_2.13.0.zip(r-4.5)
lfa_2.13.0.tgz(r-4.6-x86_64)lfa_2.13.0.tgz(r-4.6-arm64)lfa_2.13.0.tgz(r-4.5-x86_64)lfa_2.13.0.tgz(r-4.5-arm64)
lfa_2.13.0.tar.gz(r-4.7-arm64)lfa_2.13.0.tar.gz(r-4.7-x86_64)lfa_2.13.0.tar.gz(r-4.6-arm64)lfa_2.13.0.tar.gz(r-4.6-x86_64)
lfa_2.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lfa/json (API)
| # Install 'lfa' in R: |
| install.packages('lfa', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/storeylab/lfa/issues
Datasets:
- hgdp_subset - HGDP subset
On BioConductor:lfa-2.13.0(bioc 3.24)lfa-2.12.0(bioc 3.23)
snpdimensionreductionprincipalcomponentregressionopenblas
Last updated from:c956db953c. Checks:1 WARNING, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 168 | ||
| linux-devel-arm64 | OK | 173 | ||
| linux-devel-x86_64 | OK | 200 | ||
| source / vignettes | OK | 200 | ||
| linux-release-arm64 | OK | 172 | ||
| linux-release-x86_64 | OK | 160 | ||
| macos-release-arm64 | OK | 202 | ||
| macos-release-x86_64 | OK | 306 | ||
| macos-oldrel-arm64 | OK | 92 | ||
| macos-oldrel-x86_64 | OK | 241 | ||
| windows-devel | OK | 89 | ||
| windows-release | OK | 111 | ||
| windows-oldrel | OK | 102 | ||
| wasm-release | OK | 163 |
Exports:afaf_snpcenterscalelfapca_afsHWEtrunc_svd
Dependencies:BEDMatrixbitbit64clicliprcorpcorcpp11crayoncrochetdplyrgenericsgeniogluehmslatticelifecyclemagrittrMatrixpillarpkgconfigprettyunitsprogressR6RcppRcppEigenreadrrlangRSpectratibbletidyselecttzdbutf8vctrsvroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Allele frequencies | af |
| Allele frequencies for SNP | af_snp |
| Matrix centering and scaling | centerscale |
| HGDP subset | hgdp_subset |
| Logistic factor analysis | lfa |
| Defunct functions in package 'lfa'. | lfa-defunct |
| PCA Allele frequencies | pca_af |
| Hardy-Weinberg Equilibrium in structure populations | sHWE |
| Truncated singular value decomposition | trunc_svd |
