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:
- 431345 SNPs by 940 individuals: 1.5 GB needed for genotype matrix, about 9 GB to run `lfa`.
- 339100 SNPs by 1500 individuals: 1.9 GB needed for genotype matrix, about 11.5 GB to run `lfa`.
`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:
brew install gcc
If XCode installation fails, you may have to sign up on Apple Developer: https://www.ics.uci.edu/~pattis/common/handouts/macmingweclipse/allexperimental/macxcodecommandlinetools.html
Alternatively, this Installer Package for macOS R toolchain may work https://github.com/rmacoslib/r-macos-rtools/
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](https://doi.org/10.1093/bioinformatics/btv641). [arXiv](https://arxiv.org/abs/1312.2041).