Package index • LimROTS

All functions
`Boot_parallel()`	Parallel processing handling function
`Check_SummarizedExperiment()`	Check if SummarizedExperiment or data is correct
`Check_meta_info()`	Check if meta info is correct
`LimROTS()`	`LimROTS`: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics and Metabolomics Data
`Limma_bootstrap()`	Perform Linear Modeling with Covariates using Limma
`Limma_fit()`	Perform Linear Modeling with Covariates using Limma
`Limma_permutating()`	Perform Permutation-Based Linear Modeling with Covariates using Limma
`Optimizing()`	Optimize Parameters Based on Overlap Calculations
`SanityChecK()`	Sanity Check for Input Data and Parameters
`UPS1.Case4`	Spectronaut and ScaffoldDIA UPS1 Spiked Dataset case 4
`bootstrapS()`	Generate Bootstrap Samples
`bootstrapSamples_limRots()`	Generate Stratified Bootstrap Samples for limRots
`calOverlaps()`	Calculate Overlaps Between Observed and Permuted Data
`calOverlaps_slr()`	Calculate Overlaps for Single-Label Replicates (SLR)
`calculateFalseDiscoveryRate()`	Calculate False Discovery Rate (FDR) Using Permuted Values (Adjusted)
`countLargerThan()`	Count Larger Permuted Values (Modified)

Reference