Man pages for fbreitwieser/isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data
| calc.delta.score | Calculate Delta Score from Ion Score |
| calc.startpos | Recalculate peptide start positions based on protein sequence |
| calculate.dNSAF | dNSAF approximate abundance calculations. |
| calculate.emPAI | emPAI approximate abundance calculations. |
| calculate-pvalues | Calculate and Adjust Ratio and Sample p-values. |
| correct.peptide.ratios | Correct peptide ratios with protein ratios from a separate... |
| distr-methods | Functions for distribution calculations |
| fit-distr | Fit weighted and unweighted Cauchy and Normal distributions |
| getPeptideModifContext | Get context of modification |
| getPhosphoRSProbabilities | Generate input files for PhosphoRS, call it, and get... |
| getPtmInfo | Get PTM site information for idenfied proteins from public... |
| groupMemberPeptides | Peptide info for protein group members |
| human.protein.names | Info on proteins |
| IBSpectra-class | IBSpectra Class for Isobarically Tagged Quantitative MS... |
| isobar-analysis | IBSpectra analysis: Protein and peptide ratio calculation |
| isobar-data | Isobar Data packages |
| isobar-import | Loading data into IBSpectra objects using readIBSpectra |
| isobar-log | Log functions for IBSpectra objects |
| isobar-package | Analysis and quantitation of isobarically tagged MSMS... |
| isobar-plots | IBSpectra plots |
| isobar-preprocessing | IBSpectra preprocessing |
| isobar-reports | Isobar reports |
| maplot.protein | Ratio intensity plot for individual proteins |
| NoiseModel-class | NoiseModel objects |
| number.ranges | Helper function to transform number lists to ranges |
| observedKnownSites | Observed modification sites. |
| peptide.count | Peptide counts, spectral counts and sequence coverage for... |
| ProteinGroup-class | ProteinGroup objects |
| proteinInfo-methods | Methods for Function proteinInfo |
| proteinNameAndDescription | Get protein gene names and description from protein info of... |
| ratiosReshapeWide | Reshape output of proteinRatios into wide format |
| ratio-summ | Calculating and Summarizing Protein and Peptide Ratios |
| reporter.protein-methods | Get reporter protein group identifier for protein group... |
| sanitize | Helper function for LaTeX export |
| shared.ratios | Shared ratio calculation |
| shared.ratios.sign | Plot and get significantly shared ratios. |
| specificities | Peptide specificities |
| spectra.count2 | Spectral count for peptides and proteins in ProteinGroup... |
| subsetIBSpectra | Subset IBSpectra objects |
| Tlsd-class | Class '"Tlsd"' |
| TlsParameter-class | Class '"TlsParameter"' |
| utils | Isobar util functions |
| writeHscoreData | Write identifications into a format suitable for Hscore. |
| writeIBSpectra | Write IBSpectra file as CSV in a format readable by... |
