waddR-package: waddR: Statistical tests for detecting differential...

In goncalves-lab/diffexpR: Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

waddR: Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

Description

The package offers statistical tests based on the 2-Wasserstein distance for detecting and characterizing differences between two distributions given in the form of samples. Functions for calculating the 2-Wasserstein distance and testing for differential distributions are provided, as well as a specifically tailored test for differential expression in single-cell RNA sequencing data.

Details

The waddR package provides tools to address the following tasks:

1. Computation of the 2-Wasserstein distance

2. Two-sample tests to check for differences between two distributions

3. Detection of differential gene expression distributions in single-cell RNA sequencing data

1. 2-Wasserstein distance functions

The 2-Wasserstein distance is a metric to quantify the difference between two distributions, representing e.g. two different conditions A and B. The waddR package specifically considers the squared 2-Wasserstein distance which can be decomposed into location, size, and shape terms, thus providing a characterization of potential differences. It offers three functions to calculate the (squared) 2-Wasserstein distance, which are implemented in C++ and exported to R with Rcpp for faster computation. wasserstein_metric is a C++ reimplementation of the wasserstein1d function from the R package transport. The functions squared_wass_approx and squared_wass_decomp compute approximations of the squared 2-Wasserstein distance, with squared_wass_decomp also returning the decomposition terms for location, size, and shape.

See ?wasserstein_metric, ?squared_wass_aprox, and ?squared_wass_decomp as well as the accompanying paper Schefzik et al. (2020).

2. Testing for differences between two distributions

The waddR package provides two testing procedures using the 2-Wasserstein distance to test whether two distributions F_A and F_B given in the form of samples are different by testing the null hypothesis H_0: F_A = F_B against the alternative hypothesis H_1: F_A \neq F_B.

The first, semi-parametric (SP), procedure uses a permutation-based test combined with a generalized Pareto distribution approximation to estimate small p-values accurately.

The second procedure uses a test based on asymptotic theory (ASY) which is valid only if the samples can be assumed to come from continuous distributions.

See ?wasserstein.test for more details.

3. Testing for differences between two distributions in the context of single-cell RNA sequencing (scRNA-seq) data

The waddR package provides an adaptation of the semi-parametric testing procedure based on the 2-Wasserstein distance which is specifically tailored to identify differential distributions in scRNA-seq data. In particular, a two-stage (TS) approach is implemented that takes account of the specific nature of scRNA-seq data by separately testing for differential proportions of zero gene expression (using a logistic regression model) and differences in non-zero gene expression (using the semi-parametric 2-Wasserstein distance-based test) between two conditions.

See ?wasserstein.sc and ?testZeroes for more details.

References

Schefzik, R., Flesch, J., and Goncalves, A. (2020). waddR: Using the 2-Wasserstein distance to identify differences between distributions in two-sample testing, with application to single-cell RNA-sequencing data.

Author(s)

Maintainer: Julian Flesch [e-mail]

Authors:

• Roman Schefzik [e-mail]

See Also

Useful links:

• https://github.com/goncalves-lab/waddR.git

• Report bugs at https://github.com/goncalves-lab/waddR/issues

goncalves-lab/diffexpR documentation built on June 5, 2023, 10:18 p.m.