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:Wei Hao [aut], Minsun Song [aut], Alejandro Ochoa [aut, cre], John D. Storey [aut]

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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

Uses libs:
  • openblas– Optimized BLAS
Datasets:

On BioConductor:lfa-2.7.0(bioc 3.21)lfa-2.6.0(bioc 3.20)

snpdimensionreductionprincipalcomponentregressionopenblas

7.04 score 16 stars 1 packages 57 scripts 649 downloads 1 mentions 11 exports 6 dependencies

Last updated 5 months agofrom:bf41026f04. Checks:9 OK, 3 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-win-x86_64WARNINGMar 29 2025
R-4.5-mac-x86_64OKMar 29 2025
R-4.5-mac-aarch64OKMar 29 2025
R-4.5-linux-x86_64OKMar 29 2025
R-4.4-win-x86_64WARNINGMar 29 2025
R-4.4-mac-x86_64OKMar 29 2025
R-4.4-mac-aarch64OKMar 29 2025
R-4.4-linux-x86_64OKMar 29 2025
R-4.3-win-x86_64WARNINGMar 29 2025
R-4.3-mac-x86_64OKMar 29 2025
R-4.3-mac-aarch64OKMar 29 2025

Exports:afaf_snpcentercenterscalelfamodel.gofpca_afread.bedread.tped.recodesHWEtrunc_svd

Dependencies:corpcorlatticeMatrixRcppRcppEigenRSpectra

lfa Package

Rendered fromlfa.Rnwusingknitr::knitron Mar 29 2025.

Last update: 2023-06-20
Started: 2014-11-04