Perform Two-Way Orthogonal Partial Least Squares

Performs the O2PLS data integration method for two datasets yielding joint and data-specific parts for each dataset. The algorithm automatically switches to a memory-efficient approach to fit O2PLS to high dimensional data. It provides a rigorous and a faster alternative cross-validation method to select the number of components, as well as functions to report proportions of explained variation and to construct plots of the results. See Trygg and Wold (2003) and el Bouhaddani et al (2016) .


GPL-3 Build Status codecov Build Status

Welcome to the OmicsPLS package page on Github. OmicsPLS contains an implementation of O2PLS.

O2PLS is designed for integrating two high dimensional datasets and the O2PLS package is an implementation of this method.

Installing

Install the package with:

install.packages("OmicsPLS")

Note that copying the quotation marks can sometimes go wrong, type them yourself to be sure. If that doesn't work, ensure that the required packages are installed (ggplot2 and parallel). Otherwise try the development version on this GitHub repo:

require(devtools)
devtools::install_github("selbouhaddani/OmicsPLS")

Or download the source .tar.gz or the Windows binaries .zip at my ZippedPackages repo.

Loading

After installing the package, load the functions by typing

library(OmicsPLS)

Bugs, questions, complaints, etc

For questions, complaints, bugs, etc, you can e-mail me (<s.el_bouhaddani at lumc.nl>) or file an issue here at GitHub.

Citing the package

When using the OmicsPLS R-package in your research, please cite the corresponding article by running command

citation("OmicsPLS")

or copy-paste: Bouhaddani, S., Houwing-duistermaat, J., Jongbloed, G., Salo, P., Perola, M., & Uh, H.-W. (2016). Evaluation of O2PLS in Omics data integration. BMC Bioinformatics BMTL Supplement. DOI: 10.1186/s12859-015-0854-z

Atlas of science publication

Also please see http://atlasofscience.org/simultaneous-integrated-analysis-of-biological-datasets-an-evaluation-of-o2pls/ for a gentle explanation and illustration of the just mentioned article.

Updates

  • We are working on a software tutorial paper and vignette to be published soon! Please see the OmicsPLS_vignette.pdf for a walkthrough of the OmicsPLS package with real data. In the meantime just email me for more information on the package.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("OmicsPLS")

1.1.0 by Said el Bouhaddani, a month ago


Browse source code at https://github.com/cran/OmicsPLS


Authors: Said el Bouhaddani, Jeanine Houwing-Duistermaat, Geurt Jongbloed, Szymon Kielbasa and Hae-Won Uh


Documentation:   PDF Manual  


GPL-3 license


Imports ggplot2, parallel

Suggests testthat, knitr, rmarkdown, gplots


See at CRAN