DOI: 10.18129/B9.bioc.lfa  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see lfa.

Logistic Factor Analysis for Categorical Data

Bioconductor version: 3.17

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).

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

Maintainer: Alejandro Ochoa <alejandro.ochoa at duke.edu>

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biocViews DimensionReduction, PrincipalComponent, Regression, SNP, Software
Version 2.0.11
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License GPL (>= 3)
Depends R (>= 4.0)
Imports utils, methods, corpcor, RSpectra
Suggests knitr, ggplot2, testthat, BEDMatrix, genio
URL https://github.com/StoreyLab/lfa
BugReports https://github.com/StoreyLab/lfa/issues
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