Statistical Characterization of Post-translational Modifications

Documentation for package ‘MSstatsPTM’ version 1.0.0

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