Package: lfa
Title: Logistic Factor Analysis for Categorical Data
Version: 2.10.0
Authors@R: c(
    person(given = "Wei",
	   family = "Hao",
	   role = "aut",
	   email = "whao@princeton.edu"),
    person(given = "Minsun",
	   family = "Song",
	   role = "aut"),
    person(given = "Alejandro",
	   family = "Ochoa",
	   role = c("aut", "cre"),
	   email = "alejandro.ochoa@duke.edu",
           comment = c(ORCID = "0000-0003-4928-3403")),
    person(given = "John D.",
           family = "Storey",
	   role = "aut",
	   email = "jstorey@princeton.edu",
           comment = c(ORCID = "0000-0001-5992-402X"))
    )
Encoding: UTF-8
LazyData: true
Description: 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).
Imports: utils, methods, corpcor, RSpectra
Depends: R (>= 4.0)
Suggests: knitr, ggplot2, testthat, BEDMatrix, genio
VignetteBuilder: knitr
License: GPL (>= 3)
biocViews: SNP, DimensionReduction, PrincipalComponent, Regression
BugReports: https://github.com/StoreyLab/lfa/issues
URL: https://github.com/StoreyLab/lfa
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:23:35 UTC
RemoteUrl: https://github.com/bioc/lfa
RemoteRef: RELEASE_3_22
RemoteSha: 9604f60f0356bd513bc930d95097418b4eb6f8a2
NeedsCompilation: yes
Packaged: 2026-02-22 07:44:15 UTC; root
Author: Wei Hao [aut],
  Minsun Song [aut],
  Alejandro Ochoa [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4928-3403>),
  John D. Storey [aut] (ORCID: <https://orcid.org/0000-0001-5992-402X>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Built: R 4.5.2; x86_64-w64-mingw32; 2026-02-22 07:45:28 UTC; windows
Archs: x64
