Files in nignatiadis/IHWpaper
Reproduce figures in IHW paper

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/RcppExports.R R/analyze_datasets.R R/benchmarking.R R/covariate_methods.R R/ddhw_wrappers.R R/pi0_estimators.R R/plots.R R/simple_methods.R R/simulations.R R/stratified_methods.R README.md
external_data_store.txt
inst/doc/BH-explanation.R inst/doc/BH-explanation.Rmd
inst/doc/BH-explanation.html
inst/doc/IHW_bonferroni_simulations.R inst/doc/IHW_bonferroni_simulations.Rmd
inst/doc/IHW_bonferroni_simulations.html
inst/doc/benchmark_figure.R inst/doc/benchmark_figure.Rmd
inst/doc/benchmark_figure.html
inst/doc/explaining_tdr.R inst/doc/explaining_tdr.Rmd
inst/doc/explaining_tdr.html
inst/doc/grenander_vs_ecdf.R inst/doc/grenander_vs_ecdf.Rmd
inst/doc/grenander_vs_ecdf.html
inst/doc/hQTL_example.R inst/doc/hQTL_example.Rmd
inst/doc/hQTL_example.html
inst/doc/real_data_examples.R inst/doc/real_data_examples.Rmd
inst/doc/real_data_examples.html
inst/doc/real_data_examples_single_curve.R inst/doc/real_data_examples_single_curve.Rmd
inst/doc/real_data_examples_single_curve.html
inst/doc/simulations_vignette.R inst/doc/simulations_vignette.Rmd
inst/doc/simulations_vignette.html
inst/doc/stratified_histograms.R inst/doc/stratified_histograms.Rmd
inst/doc/stratified_histograms.html
inst/doc/tdr_pvalue_rejection_thresholds.R inst/doc/tdr_pvalue_rejection_thresholds.Rmd
inst/doc/tdr_pvalue_rejection_thresholds.html
inst/doc/weights_vs_filtering.R inst/doc/weights_vs_filtering.Rmd
inst/doc/weights_vs_filtering.html
inst/extdata/real_data/.DS_Store
inst/extdata/real_data/bottomly_eset.RData
inst/extdata/real_data/hammer_eset.RData
inst/extdata/real_data/hqtl_pvalue_filtered.Rds
inst/extdata/real_data/science_signaling.csv
inst/real_data_examples/.DS_Store
inst/real_data_examples/README
inst/real_data_examples/RNAseq_example_analysis.R
inst/real_data_examples/bottomly_eset.RData
inst/real_data_examples/data_examples.pdf inst/real_data_examples/hqtl_example_analysis.R inst/real_data_examples/mcp.R inst/real_data_examples/proteomics_example_analysis.R inst/real_data_examples/readme.md
inst/real_data_examples/result_files/RNAseq_benchmark.Rds
inst/real_data_examples/result_files/hQTL_benchmark.Rds
inst/real_data_examples/result_files/proteomics_benchmark.Rds
inst/simulation_benchmarks/ihw_bonferroni_du_ttest_informative_simulation_benchmark_E3.R
inst/simulation_benchmarks/ihw_bonferroni_du_ttest_informative_simulation_benchmark_E3.sh
inst/simulation_benchmarks/ihw_bonferroni_null_simulation_benchmark.R
inst/simulation_benchmarks/ihw_bonferroni_null_simulation_benchmark.sh
inst/simulation_benchmarks/ihw_bonferroni_wasserman_normal_simulations_benchmark_E3.R
inst/simulation_benchmarks/ihw_bonferroni_wasserman_normal_simulations_benchmark_E3.sh
inst/simulation_benchmarks/ihw_du_ttest_informative_simulation_benchmark.R inst/simulation_benchmarks/ihw_du_ttest_informative_simulation_benchmark_E3.R inst/simulation_benchmarks/ihw_du_ttest_informative_simulation_benchmark_grb.R inst/simulation_benchmarks/ihw_null_simulation_benchmark.R inst/simulation_benchmarks/ihw_null_simulation_benchmark_E3.R inst/simulation_benchmarks/ihw_null_simulation_benchmark_grb.R inst/simulation_benchmarks/ihw_wasserman_normal_prds_simulations_benchmark.R
inst/simulation_benchmarks/ihw_wasserman_normal_prds_simulations_benchmark.sh
inst/simulation_benchmarks/ihw_wasserman_normal_simulations_benchmark.R inst/simulation_benchmarks/ihw_wasserman_normal_simulations_benchmark_E3.R inst/simulation_benchmarks/ihw_wasserman_normal_simulations_benchmark_grb.R
inst/simulation_benchmarks/result_files/.DS_Store
inst/simulation_benchmarks/result_files/.Rapp.history
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_1.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_10.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_11.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_12.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_13.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_14.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_15.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_16.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_17.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_18.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_19.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_2.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_20.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_3.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_4.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_5.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_6.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_7.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_8.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_du_ttest_informative/par_setting_9.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_1.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_10.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_2.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_3.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_4.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_5.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_6.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_7.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_8.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_null/par_setting_9.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_1.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_10.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_2.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_3.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_4.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_5.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_6.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_7.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_8.Rds
inst/simulation_benchmarks/result_files/ihw_bonf_wasserman_normal/par_setting_9.Rds
inst/simulation_benchmarks/result_files/ihw_du_ttest_inform_simulation_benchmark.Rds
inst/simulation_benchmarks/result_files/ihw_du_ttest_inform_simulation_benchmark_E3.Rds
inst/simulation_benchmarks/result_files/ihw_du_ttest_inform_simulation_benchmark_grb.Rds
inst/simulation_benchmarks/result_files/ihw_null_simulation_benchmark.Rds
inst/simulation_benchmarks/result_files/ihw_null_simulation_benchmark_E3.Rds
inst/simulation_benchmarks/result_files/ihw_null_simulation_benchmark_grb.Rds
inst/simulation_benchmarks/result_files/ihw_wasserman_normal_simulation_benchmark.Rds
inst/simulation_benchmarks/result_files/ihw_wasserman_normal_simulation_benchmark_E3.Rds
inst/simulation_benchmarks/result_files/ihw_wasserman_normal_simulation_benchmark_grb.Rds
inst/simulation_benchmarks/result_files/null_simulation_benchmark.Rds
man/analyze_dataset.Rd man/bh.Rd man/bonf.Rd man/clfdr.Rd man/continuous_wrap.Rd man/ddhf.Rd man/du_ttest_sim.Rd man/gbh.Rd man/ihw_naive.Rd man/lsl_pi0_est.Rd man/null_sim.Rd man/pretty_legend.Rd man/run_evals.Rd man/scott_fdrreg.Rd man/storey_qvalue.Rd man/stratified_bh.Rd man/tst_pi0_est.Rd man/wasserman_normal_prds_sim.Rd man/wasserman_normal_sim.Rd
src/.gitignore
src/RcppExports.cpp
src/ddhf.cpp
tests/testthat.R tests/testthat/test_analyze_datasets.R tests/testthat/test_sim_benchmarks.R vignettes/BH-explanation.Rmd vignettes/IHW_bonferroni_simulations.Rmd vignettes/benchmark_figure.Rmd vignettes/explaining_tdr.Rmd vignettes/grenander_vs_ecdf.Rmd vignettes/hQTL_example.Rmd vignettes/real_data_examples.Rmd vignettes/real_data_examples_single_curve.Rmd vignettes/simulations_vignette.Rmd vignettes/stratified_histograms.Rmd vignettes/tdr_pvalue_rejection_thresholds.Rmd vignettes/weights_vs_filtering.Rmd
nignatiadis/IHWpaper documentation built on May 23, 2017, 2:51 p.m.