PhysioSpace Methods

PhysioSpace is a robust statistical method for relating high dimensional omics data.^[Lenz, Michael, et al. "PhysioSpace: relating gene expression experiments from heterogeneous sources using shared physiological processes." PLoS One 8.10 (2013): e77627]. It is designed to take advantage of the vast availability of public omics data, which in combination with statistical approaches make a potent tool capable of analyzing heterogenious biological data sets.

PhysioSpaceMethods is a R package which provides an implementation of PhysioSpace method alongside other handy functions for making PhysioSpace an accessible tool for R users.

Installation Instructions

You can install this package by:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_gitlab("jrc-combine/PhysioSpaceMethods", host = "git.rwth-aachen.de", build_manual = TRUE, build_vignettes = TRUE)

Usage Instructions

PhysioSpaceMethods can map user samples inside a physiological space, calculated prior from a compendium of known samples. Explanation of how to use this package is provided in a vignette accessible by:

browseVignettes(package = "PhysioSpaceMethods")

Test Environments

The package was tested with R 3.5.1 on Windows 10, Mac OS X (10.12.6) and Linux (CentOS 7.4).