Package: lfa 2.7.0
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_2.7.0.tar.gz
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lfa_2.7.0.tar.gz(r-4.5-noble)lfa_2.7.0.tar.gz(r-4.4-noble)
lfa_2.7.0.tgz(r-4.4-emscripten)lfa_2.7.0.tgz(r-4.3-emscripten)
lfa.pdf |lfa.html✨
lfa/json (API)
NEWS
| # 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
- hgdp_subset - HGDP subset
On BioConductor:lfa-2.7.0(bioc 3.21)lfa-2.6.0(bioc 3.20)
snpdimensionreductionprincipalcomponentregressionopenblas
Last updated 3 months agofrom:bf41026f04. Checks:8 OK, 3 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win-x86_64 | WARNING | Jan 28 2025 |
| R-4.5-mac-x86_64 | OK | Jan 28 2025 |
| R-4.5-mac-aarch64 | OK | Jan 28 2025 |
| R-4.5-linux-x86_64 | OK | Jan 28 2025 |
| R-4.4-win-x86_64 | WARNING | Jan 28 2025 |
| R-4.4-mac-x86_64 | OK | Jan 28 2025 |
| R-4.4-mac-aarch64 | OK | Jan 28 2025 |
| R-4.3-win-x86_64 | WARNING | Jan 28 2025 |
| R-4.3-mac-x86_64 | OK | Jan 28 2025 |
| R-4.3-mac-aarch64 | OK | Jan 28 2025 |
Exports:afaf_snpcentercenterscalelfamodel.gofpca_afread.bedread.tped.recodesHWEtrunc_svd
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 |
| PCA Allele frequencies | pca_af |
| Hardy-Weinberg Equilibrium in structure populations | sHWE |
| Truncated singular value decomposition | trunc_svd |
