Abstract
BackgroundHigh throughput microfluidic protocols in single cell RNA sequencing (scRNA-seq) collect mRNA counts from up to one million individual cells in a single experiment; this enables high resolution studies of rare cell types and cell development pathways. Determining small sets of genetic markers that can identify specific cell populations is thus one of the major objectives of computational analysis of mRNA counts data. Many tools have been developed for marker selection on single cell data; most of them, however, are based on complex statistical models and handle the multi-class case in an ad-hoc manner.ResultsWe introduce RankCorr, a fast method with strong mathematical underpinnings that performs multi-class marker selection in an informed manner. RankCorr proceeds by ranking the mRNA counts data before linearly separating the ranked data using a small number of genes. The step of ranking is intuitively natural for scRNA-seq data and provides a non-parametric method for analyzing count data. In addition, we present several performance measures for evaluating the quality of a set of markers when there is no known ground truth. Using these metrics, we compare the performance of RankCorr to a variety of other marker selection methods on an assortment of experimental and synthetic data sets that range in size from several thousand to one million cells.ConclusionsAccording to the metrics introduced in this work, RankCorr is consistently one of most optimal marker selection methods on scRNA-seq data. Most methods show similar overall performance, however; thus, the speed of the algorithm is the most important consideration for large data sets (and comparing the markers selected by several methods can be fruitful). RankCorr is fast enough to easily handle the largest data sets and, as such, it is a useful tool to add into computational pipelines when dealing with high throughput scRNA-seq data. RankCorr software is available for download at https://github.com/ahsv/RankCorrwith extensive documentation.
Highlights
High throughput microfluidic protocols in single cell RNA sequencing collect mRNA counts from up to one million individual cells in a single experiment; this enables high resolution studies of rare cell types and cell development pathways
Our results are of two types: (i) algorithmic performance guarantees for RANKCORR and (ii) empirical performance of RANKCORR and its comparison algorithms on scRNA-seq data sets
Results on the ZHENGFULL and ZHENGFILT data sets Here, we examine the data set consisting of 68k peripheral blood mononuclear cells (PBMCs) from [2]; it contains data from more than 30 times the number of cells in either the PAUL or ZEISEL data sets
Summary
High throughput microfluidic protocols in single cell RNA sequencing (scRNA-seq) collect mRNA counts from up to one million individual cells in a single experiment; this enables high resolution studies of rare cell types and cell development pathways. Modern scRNA-seq experiments produce massive amounts of integer valued counts data These scRNA-seq data exhibit high variance and are sparse (often, approximately 90% of the reads are 0 [4]) for both biological (e.g. transcriptional bursting) and technical (e.g. 3’ bias in UMI based sequencing protocols) reasons. Those characteristics, in combination with the integer valued quality of the counts and the high dimensionality of the data (often, 20,000 genes show nonzero expression levels in an experiment), are such that scRNA-seq data do not match many of the models that underlie common data analysis techniques. Many specialized tools have been developed to answer biological questions with scRNA-seq data
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