Logistic factor analysis


To install latest version on Bioconductor, open R and type:

if (!requireNamespace("BiocManager", quietly = TRUE))


You can also install development version from GitHub this way:


Apple OS X users, see Troubleshooting below.

Data input

We recommend using the genio or BEDMatrix packages to read genotype data into an R matrix.

Be warned that genotype matrices from genio and some lfa functions require a lot of memory. As a rule of thumb, the in memory sizes of a few relevant genotype matrices:

BEDMatrix inputs consume much less memory but can be slower otherwise.


Apple OS X users may experience a problem due to Fortran code that is included in this package. You must install the X code command line tools (XCode CLI) and gfortran. Try the following commands on terminal:

xcode-select --install 
brew install gcc

If XCode installation fails, you may have to sign up on Apple Developer:

Alternatively, this Installer Package for macOS R toolchain may work


Hao, Wei, Minsun Song, and John D. Storey. "Probabilistic Models of Genetic Variation in Structured Populations Applied to Global Human Studies." Bioinformatics 32, no. 5 (March 1, 2016): 713–21. doi:10.1093/bioinformatics/btv641. arXiv.

StoreyLab/lfa documentation built on March 7, 2024, 9:59 p.m.