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OmicsPLS Short Course

2023 Edition | Said el Bouhaddani and Jeanine Houwing-Duistermaat

Instructions to download material

Please click on one of the links below. Download the files: right click on the 'download' button and click "save link as". Check that the extension is '.html' resp. '.RData'.

The course slides are in this folder. Click on one of the slides and right click on the download button + "save link as".

Alternatively, download the whole repo by clicking above on "code" and then "download ZIP".

Installing R packages

First update your R to at least version 4.0.5. Run R.version to see which version you have. It's recommended to update to the most recent version. Please install the required packages before the course starts.

First run

if(compareVersion(paste0(R.Version()[c("major","minor")], collapse = "."), "4.0.5") < 0) cat("Please update R to the latest version (at least 4.0.5)\n")
req_pack <- c("MASS", "parallel", "tidyverse", "magrittr", 
              "OmicsPLS", "httr", "disgenet2r", "GGally")
if(sum(!(req_pack %in% installed.packages()[,1])) > 0){
  cat("\nThe following packages are missing:\n")
req_pack[which(!(req_pack %in% installed.packages()[,1]))]
} else cat("\nNo packages missing.\n")

Then select from the commands below to install the missing packages (if any).

install.packages("MASS")      # statistical tools, such as lda
install.packages("tidyverse") # dataset & viz tools
install.packages("magrittr")  # pipe operators
install.packages("httr")      # http tools
install.packages("GGally")    # extra ggplot2 tools
install.packages("OmicsPLS")  # data integration toolkit

install.packages("remotes")   # install experimental packages
remotes::install_bitbucket("ibi_group/disgenet2r") # experimental R package

Installing disgenet2r

NOTE If the installation described below was not successful, it will not be a problem for the course.

To install disgenet2r, you need to be able to compile packages from source. Practically, this means that you need to install some additional tools. You will need Rtools (Windows) or Xcode (MacOS) which have separate installation instructions. Please first check whether they are already installed, e.g. by looking at the list of installed programs.

Next, check whether you have the package SPARQL (e.g. by running library(SPARQL)). If not, you need to install this package from the CRAN archive: install.packages("https://cran.r-project.org/src/contrib/Archive/SPARQL/SPARQL_1.16.tar.gz", repos=NULL, type="source").

Finally, install disgenet2r with remotes::install_bitbucket("ibi_group/disgenet2r").

Quick troubleshooting

  • There is a problem with the html or other files. If the one-by-one download didn't work, try downloading the whole repository as a zip file. Extract the zip to a folder and try again. If the issue remains, please contact me (email: s.elbouhaddani at umcutrecht.nl).
  • I get "These packages have more recent versions available" with a list of packages. The best way is to enter 1 or 2 (All or CRAN only) and update old packages. In principle, you should be able to still install all packages while selecting 3 (none), but it's recommended to regularly update R and the packages.
  • I get "package 'xxx' is not available (for R version x.y.z)" when trying to install a package. Most likely this is due to an outdated R version. Please update your R to at least version 4.0.5. Run R.version to see which version you have. It could also be that a dependent package is missing, check all errors, warnings and messages to see which package is the culprit. Note that disgenet2r needs a special approach, described above.
  • I get another strange message. Did you update to at least R 4.0.5? When trying to install disgenet2r, do you have Rtools or Xcode installed? If yes, please contact me (email: s.elbouhaddani at umcutrecht.nl) or open a new issue (see button Issues above). Please carefully describe what you did, and also copy-paste the output of sessionInfo() in your message.

Assignments

The exercises are given inline. They typically refer to the next code block. The answers and code output are given in the file ending with "ANSWERS.html".

Evaluation form

Please fill in the short evaluation form. Your feedback is much appreciated.

Click here for the form (the form will be activated at the end of the course).

Reading material

Bouhaddani, S., Uh, HW., Jongbloed, G. et al. Integrating omics datasets with the OmicsPLS package. BMC Bioinformatics 19, 371 (2018). https://doi.org/10.1186/s12859-018-2371-3

Vincenzo Borelli, Valerie Vanhooren, Emanuela Lonardi, Karli R. Reiding, Miriam Capri, Claude Libert, Paolo Garagnani, Stefano Salvioli, Claudio Franceschi, and Manfred Wuhrer. Plasma N-Glycome Signature of Down Syndrome. Journal of Proteome Research 2015 14 (10), 4232-4245. https://doi.org/10.1021/acs.jproteome.5b00356

Bacalini, M. G., Gentilini, D., Boattini, A., Giampieri, E., Pirazzini, C., Giuliani, C., Fontanesi, E., Scurti, M., Remondini, D., Capri, M., Cocchi, G., Ghezzo, A., Del Rio, A., Luiselli, D., Vitale, G., Mari, D., Castellani, G., Fraga, M., Di Blasio, A. M., … Garagnani, P. (2015). Identification of a DNA methylation signature in blood cells from persons with Down Syndrome. Aging, 7(2), 82–96. https://doi.org/10.18632/aging.100715

Cook, R. D. (2022). A slice of multivariate dimension reduction. Journal of Multivariate Analysis, 188, 104812. https://doi.org/10.1016/j.jmva.2021.104812

Gu, Z., el Bouhaddani, S., Pei, J. et al. Statistical integration of two omics datasets using GO2PLS. BMC Bioinformatics 22, 131 (2021). https://doi.org/10.1186/s12859-021-03958-3

el Bouhaddani, S., Uh, H.-W., Jongbloed, G., & Houwing‐Duistermaat, J. (2022). Statistical integration of heterogeneous omics data: Probabilistic two‐way partial least squares (PO2PLS). Journal of the Royal Statistical Society: Series C (Applied Statistics). https://doi.org/10.1111/rssc.12583