lfa
Logistic Factor Analysis for Categorical Data
DOI: 10.18129/B9.bioc.lfa
Bioconductor version: Release (3.19)
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("lfa")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, PrincipalComponent, Regression, SNP, Software |
| Version | 2.4.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | gcatest |
| Suggests Me | jackstraw |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lfa_2.4.0.tar.gz |
| Windows Binary (x86_64) | lfa_2.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | lfa_2.4.0.tgz |
| macOS Binary (arm64) | lfa_2.4.0.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 |