tpq/propr: An R package to calculate proportionality and other measures for compositional data

The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, conventional correlation measures lack validity when applied to compositional data, including count data generated by next-generation sequencing. Here we implemented valid alternatives for measuring association between vectors of compositional data. These include several metrics for proportionality, such as phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. It also implements a regularized version of logratio partial correlations [Jin et al (2023) <DOI:10.57645/20.8080.02.8>]. Moreover, this package implements several metrics for differential proportionality [Erb et al (2017) <DOI:10.1101/134536>].

install.packages("remotes")
remotes::install_github("tpq/propr")