Statistical Methods for Chemoproteomics Dose-Response Analysis

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Documentation for package ‘MSstatsResponse’ version 1.0.0

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

Help Pages

.extractTemplatesFromData	Helper function to extract template profiles from user data
bootstrapIC50	Bootstrap IC50 Estimates and Confidence Interval (ratio scale)
bootstrapIC50LogScale	Bootstrap IC50 Estimates and Confidence Interval (log scale)
convertGroupToNumericDose	Convert MSstats GROUP labels to numeric dose in nM and extract drug name
DIA_MSstats_Normalized	Example pre-processed DIA-MS dataset
doseResponseFit	Drug-protein interaction detection tested by F-test (fitted curve vs average response)
fitIsotonicRegression	Fit Isotonic Regression Model
futureExperimentSimulation	Test future experimental design using simulated data with user-defined or default templates
MSstatsPrepareDoseResponseFit	Prepare data for dose-response fitting with isotonic regression
plotHitRateMSstatsResponse	Plot hit rates by category
plotIsotonic	Plot Isotonic Regression Model
predictIC50	Predict IC50 (dose where response = target) for each protein and drug
predictIC50Parallel	Parallel version of predictIC50 function
simulateChemoProteinLevelNonParametric	Simulate chemoproteomics data at the protein level - non-parametric approach
visualizeResponseProtein	Plot isotonic regression fit with optional IC50 for a single protein and drug