Statistical Characterization of Post-translational Modifications


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Documentation for package ‘MSstatsPTM’ version 1.0.0

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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
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
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