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lfa

Logistic Factor Analysis for Categorical Data


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("lfa")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("lfa")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("lfa")
lfa Package PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DimensionReduction, PrincipalComponent, Regression, SNP, Software
Version 2.2.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL (>= 3)
Depends R (>= 4.0)
Imports utils, methods, corpcor, RSpectra
System Requirements
URL https://github.com/StoreyLab/lfa
Bug Reports https://github.com/StoreyLab/lfa/issues
See More
Suggests knitr, ggplot2, testthat, BEDMatrix, genio
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Depends On Me
Imports Me gcatest
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package lfa_2.2.0.tar.gz
Windows Binary lfa_2.2.0.zip (64-bit only)
macOS Binary (x86_64) lfa_2.2.0.tgz
macOS Binary (arm64) lfa_2.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lfa
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lfa
Bioc Package Browser https://code.bioconductor.org/browse/lfa/
Package Short Url https://bioconductor.org/packages/lfa/
Package Downloads Report Download Stats