Reproduce figures in IHW paper


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Documentation for package ‘IHWpaper’ version 1.36.0

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analyze_dataset analyze_dataset: Basically performs preprocessing and then returns analyzed RNASeq dataset (diff. expression) , i.e. the DESeq2 result whose p-values and baseMean statistics can then be used with IHW
bh bh: Wrapper for Benjamini Hochberg
bonf bonf: Wrapper for Bonferroni
clfdr clfdr: Cai's local fdr based method
continuous_wrap Benchmarking wrapper: Given a multiple testing method, convert it so that it takes a simulation object (see simulation function) and a nominal level alpha as inputs
ddhf ddhf: Greedy independent filtering
du_ttest_sim t-test simulation: Simulate rowwise t-tests
du_ttest_sim_fun t-test simulation: Simulate rowwise t-tests
gbh gbh: Grouped Benjamini Hochberg
ihw_5fold IHW wrappers
ihw_5fold_reg IHW wrappers
ihw_bonf_5fold_reg IHW wrappers
ihw_ecdf_5fold IHW wrappers
ihw_naive IHW wrappers
ihw_storey_5fold IHW wrappers
lsl_gbh gbh: Grouped Benjamini Hochberg
lsl_pi0_est LSL (Least-Slope) pi0 estimator
null_sim Null simulation: Generate uniformly distributed p-values and covariates
null_sim_fun Null simulation: Generate uniformly distributed p-values and covariates
pretty_legend helper function to create nice legends
run_evals run_evals: Main function to benchmark FDR methods on given simulations.
scott_fdrreg scott_fdrreg: Wrapper for FDR regression (https://github.com/jgscott/FDRreg)
storey_qvalue storey_qvalue: Wrapper for Storey's qvalue package
stratified_bh stratified_bh: Stratified Benjamini Hochberg
tst_gbh gbh: Grouped Benjamini Hochberg
tst_pi0_est TST (Two-Step) pi0 estimator
wasserman_normal_prds_sim Normal PRDS simulation: Covariate is effect size under alternative, there are latent factors driving PRDS correlations among hypotheses
wasserman_normal_prds_sim_fun Normal PRDS simulation: Covariate is effect size under alternative, there are latent factors driving PRDS correlations among hypotheses
wasserman_normal_sim Normal simulation: Covariate is effect size under alternative
wasserman_normal_sim_fun Normal simulation: Covariate is effect size under alternative