Man pages for MSstatsPTM
Statistical Characterization of Post-translational Modifications
| adjustProteinLevel | Adjust differential analysis result with respect to protein... |
| annotSite | Annotate modification site |
| estimateAbundance | Estimate log2-abundances of PTM sites or proteins |
| extractMeanDiff | Compare mean abundances for PTM sites (or proteins) across... |
| 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... |
| 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 |
