This repository contains some scripts to assess different methods of choosing the number of PCs to retain. The text directory contains LaTeX files for the report, a compiled PDF of which can be found here. The simulations directory contains R scripts for performing the basic simulations:

• functions.R, a central R script containing definitions of useful functions for the simulations.
• sim_gaussclust.R, a template for simulations of clusters with Gaussian noise.
• sim_trajectory.R, a tempalte for simulations of trajectories between multiple nodes.
• submitter.sh, a Bash script for SLURM job submission of the simulations.
• plot_results.R, an R script to generate the plots.
• simulate_noise.R, an R script examining the effect of removing biological noise.

The real directory contains R scripts for performing the real data-based simulations:

• proc_kolod.R, an R script for pre-processing the mESC data set.
• proc_pbmc4k.R, an R script for pre-processing the PBMC data set.
• run_kolod.R, a template for performing simulations based on the mESC data set.
• run_pbmc4k.R, a template for performing simulations based on the PBMC data set.
• submitter.sh, a Bash script for SLURM job submission of the simulations.
• plot_results.R, an R script to generate the plots.

In addition, batching/batching.Rmd contains an example of how batch removal in the presence of zeroes can distort the PCA results.