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Bioconductor - lfa (development version)

This is the development version of lfa; for the stable release version, see lfa.

Bioconductor version: Development (3.22)

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] ORCID: 0000-0003-4928-3403 , John D. Storey [aut] ORCID: 0000-0001-5992-402X

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

To install this package, start R (version "4.5") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("lfa")

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

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

browseVignettes("lfa")

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

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