This is a package which reproduces all IHW paper figures (as well as some additional figures for presentations etc.).
All vignettes can be found in the /vignettes directory. For the vignettes which reproduce figures in our manuscript, we also provide a link to the rendered html page below:
- Figure 1: Stratified Histograms
- Figure 2, S1, S2 : Benchmarking result
- Figure 3: Schematic figure, no code used for its generation
- Figures S3 and S4: Explaining tdr
- Figure S5: IHW-Bonferroni simulations
You can install the package as follows:
library("devtools")
# install IHW
install_github("vladchimescu/lpsymphony", subdir="lpsymphony")
install_github("nignatiadis/IHW")
# install FDRreg, version on CRAN is outdated
install_github(repo= "jgscott/FDRreg", subdir="R_pkg/", ref = "a63cebae6faecb1fb0ebee634195296f39faa11b")
# Bioconductor prerequisites
source("http://bioconductor.org/biocLite.R")
biocLite(c("genefilter","DESeq2","qvalue","Biobase",
"BiocParallel","airway","pasilla", "BiocStyle"))
# finally install this package
install_github("nignatiadis/IHWpaper")
Afterwards you can view the pre-built vignettes or rebuild them yourself.
Notice that the vignettes load binary .Rds files which are stored in inst/real_data_examples/result_files and inst/simulations_benchmarks/result_files. These have been generated by longer lasting jobs, the code for which can be found in inst/real_data_examples and inst/simulation_benchmarks.