FDR-corrected SCCA R scripts
The R scripts in the
examples directory perform the simulation studies described in Gossmann et. al. FDR-Corrected Sparse Canonical Correlation Analysis with Applications to Imaging Genomics (2017). Code to generate visualizations from the simulation results, as presented in the paper, is provided in this repository as well.
The R scripts have been written with the intention of running them on the high performance computing cluster Cypress at Tulane University, which uses the Slurm resource management system.
Many functions (see the
R directory), which are used to implement the simulations in the
examples directory, are provided in form of an R package. The R package
FDRcorrectedSCCA can be installed using
devtools in R (see below). However, this should not be necessary in order to run the scripts from the
examples directory, because within those scripts all functions from the
FDRcorrectedSCCA package are loaded with
However, if you have trouble running the example scripts (ahem Windows ahem...), try installing the required functions as an R package following the instructions below. In that case the line
devtools::load_all() has to be replaced with
library(FDRcorrectedSCCA) in the example codes.
The R package
FDRcorrectedSCCA can be installed form a running R session with:
# install.packages("devtools") # if devtools is not installed library(devtools) install_github("agisga/FDRcorrectedSCCA")
Development workflow - Manual installation of the R package
devtoolsR package (if you don't have it installed already):
Open the file
FDRcorrectedSCCA.Rprojin RStudio (if no Rproj file is available, you can create the Rproj file from RStudio via
File > New Project > Existing Directory).
Still in RStudio press CTRL-Shift-B. (If any of steps 1-4 fail, you are probably missing some other R packages, see the Error or Warning messages. Install the missing packages and try again from step 2.)