The data and results folder are not made public before publication.
To access those folders, please contact : mehran dot karimzadeh at uhnresearch dot ca
The analysis relies on the following R packages:
install.packages("devtool")
require(devtools)
install_github("AbHAC", username="mehrankr")
install_guthub("KeggPA", username="mehrankr")
install.packages("ggplot2")
install.packages("pheatmap")In linux/mac environment, change your directory to the src folder.
You would need data and results folder (not provided publicly) in order to run the scripts.
Rscript pathway_analysis.R 0.05 1
#The first number of the FDR cutoff threshold
#The second number is the minimum number of patients in gene must be mutated in so it is included in the analysis
Rscript abhac_analysis.R 0.05 1
#Parameters are similar to before
#You can also try:
Rscript abhac_analysis.R -h
Rscript pathway_analysis.R -h