Package: lfa
Title: Logistic Factor Analysis for Categorical Data
Version: 2.11.3
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: methods, corpcor, RSpectra, BEDMatrix, genio
Depends: R (>= 4.0)
Suggests: knitr, rmarkdown, ggplot2, testthat
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: 7.3.3
Config/pak/sysreqs: libx11-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-01-29 15:44:55 UTC
RemoteUrl: https://github.com/bioc/lfa
RemoteRef: HEAD
RemoteSha: 21a47b5c330ea4d6d70c2b545e60370039b50466
NeedsCompilation: yes
Packaged: 2026-01-30 04:11:24 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 4.6.0; x86_64-w64-mingw32; 2026-01-30 04:12:37 UTC; windows
Archs: x64
