SparseLogisticPCA

This is an implementation of the sparse logistic PCA algorithm from "Sparse logistic principal components analysis for binary data" by Lee, Huang, and Hu (2010). It uses the uniform bound for the log likelihood. The function is in the file sparse_logistic_pca.R.

I attempted to recreate the SNP data that was used as an example in the paper. The SNP data comes from release 16 of HapMap data. I used the full, non-redundant data. The list of SNPs used is in table S1 of this paper and in the file locations.csv. The data was manipulated using the file combineData.R. The final binary data is in SNPBinaryMatrix.csv

I was not able to perfectly recreate the dataset that Lee, et al. did, but the results are similar.