This repository contains code for further development of the mutual nearest neighbours (MNN) batch correction method, as implemented in the mnnCorrect and fastMNN functions in the scran package.
It is based on the code at https://github.com/MarioniLab/MNN2017, which accompanies the paper Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors by Haghverdi et al. (2018).
To run the simulations, enter the simulations/ directory and run:
cluster_sim.R, which simulates a variety of scenarios involving orthogonal batch effects.nonorth_sim.R, which simulates some pathological non-orthogonal batch effects.
Three real data analyses are available - haematopoiesis, pancreas and droplet.
Each subdirectory will usually contain:
prepareData.R, to download, pre-process and normalize the data.plotCorrections.R, to perform the batch correction and visualize the result with t-SNE plots.
Data file downloads are performed using the BiocFileCache package to save time and bandwidth. This will cache the files locally after the initial download, and reuse the cached versions when the script is re-run.