lfa

The software tool "lfa" (logistic factor analysis) addresses the challenge of analyzing genome-wide genotype data from individuals of diverse ancestries, focusing on the complex population structure without necessarily interpreting admixture proportions. This Bioconductor R package introduces two probabilistic models alongside computationally efficient algorithms for their estimation. Initially, it leverages principal component analysis to estimate a general model encompassing the Pritchard-Stephens-Donnelly admixture model. Recognizing limitations in this approach, lfa advances a novel framework for logistic factor analysis, directly modeling the logit transformation of genotype probabilities through latent variables that reflect population structure.