Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca

Abstract

Summary: Motivated by theoretical and practical issues that arise when applying Principal component analysis (PCA) to count data, Townes et al. introduced “Poisson GLM-PCA”, a variation of PCA adapted to count data, as a tool for dimensionality reduction of single-cell RNA sequencing (scRNA-seq) data. However, fitting GLM-PCA is computationally challenging. Here we study this problem, and show that a simple algorithm, which we call “Alternating Poisson Regression” (APR), produces better quality fits, and in less time, than existing algorithms. APR is also memory-efficient and lends itself to parallel implementation on multi-core processors, both of which are helpful for handling large scRNA-seq datasets. We illustrate the benefits of this approach in three publicly available scRNA-seq datasets. The new algorithms are implemented in an R package, fastglmpca.