Contents
This website contains the short course “Co-data learning: the group-regularized ridge and elastic net”
Preparation
Please install the packages GRridge:
source("https://bioconductor.org/biocLite.R")
biocLite("BiocInstaller") # if it asks to update packages, type n
biocLite("BiocGenerics") # if it asks to update packages, type n
install.packages(c("devtools", "foreach", "curl", "Matrix"))
library(devtools)
install_github("markvdwiel/GRridge")
and gren:
library(devtools)
install_version("Rcpp", version = "0.12.14", repos = "http://cran.us.r-project.org")
# R might have to restart when installing Rcpp
library(devtools)
install.packages("plyr")
install_github("magnusmunch/gren") # if it asks to install Rtools, accept
# you might have to run the previous line again after installation of Rtools
If you encounter any problems, please don’t hesitate to contact m.munch@vumc.nl or mark.vdwiel@vumc.nl
Data
The data for the GRridge part of the practical are included in the package
The data files for the gren part of the practical are found here:
Fitted models cervical cancer data
Fitted models colorectal cancer data
Practicals including Exercises
The practicals are found here:
Slides
Slides on Methodology:
Co-Data learning with empirical Bayes: GRridge and gren