MSstatsPTM              MSstatsPTM: A package for statistical
                        characterization of PTMs
PTMcompareMeans         Compare mean abundances for all PTM sites
                        across conditions
PTMestimate             Estimate log2-abundances of PTM sites and
                        proteins
PTMlocate               Annotate modified sites with associated
                        peptides
PTMnormalize            Normalization of log2-intensities across MS
                        runs
PTMsimulateExperiment   Simulate PTM quantification experiments
PTMsummarize            Site-level summarization
adjustProteinLevel      Adjust differential analysis result with
                        respect to protein abundance
annotSite               Annotate modification site
estimateAbundance       Estimate log2-abundances of PTM sites or
                        proteins
extractMeanDiff         Compare mean abundances for PTM sites (or
                        proteins) across conditions
fitLinearModel          Fit linear model
fixedGroup              Linear model with group effect
fixedGroupBatch         Linear model with group and batch effects
locateMod               Locate modified sites with a peptide
simulatePeaks           Simulate peak log2-intensities
simulateSites           Simulate peak log-intensities for PTM sites
simulateSummarization   Simulate site-level summarization for PTM
                        experiment
summarizeFeatures       Summarization for one site
tidyEstimates           Extract estimate of group effect
tidyFasta               Read and tidy a FASTA file
