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 individualspecific allele frequencies using the population structure. Lastly, a structured HardyWeinberg equilibrium (HWE) test is developed, which quantifies the goodness of fit of the genotype data to the estimated population structure, via the estimated individualspecific allele frequencies (all of which generalizes traditional HWE tests).
Package details 


Bioconductor views  DimensionReduction PrincipalComponent Regression SNP 
Maintainer  
License  GPL (>= 3) 
Version  2.0.10 
URL  https://github.com/StoreyLab/lfa 
Package repository  View on GitHub 
Installation 
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