independencepvalue-experiments

Code to reproduce simulation results and gene expression data analysis results from the article.

Package

independencepavlue_0.0.2.tar.gz contains the R package independencepavlue used to implement the proposed selective inference approach in the article.

Simulation

Simulation codes and results are stored in the folders Simulationcodes and Simulationresults, respectively.

Gene expression data analysis

We use the data from DREAM5 network inference challenge. For user convenience we provide the relevant data in the subfolder DREAM5data, under Realdatacodes. The subsubfolders DREAM5data/Training and DREAM5data/goldstandardedgesonly contain data pertaining to our article, and are downloaded from training data and Evaluation scripts, respectively. Running Realdataanalysis.R in Realdatacodes produces the gene expression data analysis results, that are stored in folder Realdataresults.

Figures

Figure codes and figures are stored in the folders Figures_codes and Figures, respectively.

1. Figure 1(a)-(b): Figure_1(a)-(b).R produces this plot.
2. Figure 1(c): Running Simulation1(c).R produces the simulation results. Figure1(c).R produces Figure 1(c).
3. Figure 2: Running Simulation2.R produces the simulation results. Figure2.R produces Figure 2.
4. Figures 3-4: Running Simulation3&4.R produces the simulation results. Figure3.R and Figure_4.R produces Figures 3 and 4.
5. Figure 5: Figure5.R produces Figure 5 using the data in folder Realdata_results.
6. Figure 6: Figure6.R produces Figure 6 using the data in folder Realdata_results.
7. Figure S1: Running SimulationS1variancefiltering.R and SimulationS1meanfiltering.R produces the simulation results and Figure_S1.R produces Figure S1.
8. Figure S2: Running SimulationS2.R produces the simulation results. FigureS2.R produces Figure S2.
9. Figure S3: Running SimulationS3.R produces the simulation results. FigureS3.R produces Figure S3.
10. Figure S4: Running SimulationS4.R produces the simulation results. FigureS4.R produces Figure S4.
11. Figure S5: Running SimulationS5.R produces the simulation results. FigureS5.R produces Figure S5.
12. Figure S6: Running SimulationS6.R produces the simulation results. FigureS6.R produces Figure S6.