A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics and Metabolomics Data

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Documentation for package ‘LimROTS’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

bootstrapS	Generate Bootstrap Samples
bootstrapSamples_limRots	Generate Stratified Bootstrap Samples for limRots
Boot_parallel	Parallel processing handling function
calculateFalseDiscoveryRate	Calculate False Discovery Rate (FDR) Using Permuted Values (Adjusted)
calOverlaps	Calculate Overlaps Between Observed and Permuted Data
calOverlaps_slr	Calculate Overlaps for Single-Label Replicates (SLR)
Check_meta_info	Check if meta info is correct
Check_SummarizedExperiment	Check if SummarizedExperiment or data is correct
countLargerThan	Count Larger Permuted Values (Modified)
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
LimROTS	'LimROTS': A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics and Metabolomics Data
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