Man pages for eahrne/SpectroX
Proteotypic peptide selection and SRM/PRM/HRM panel creation
| barplotPeptidesPerProtein | plot ranking metric vs peptide (per protein) barplot |
| barplotPetideCountPerProtein | plot peptide count per protein |
| createComplementaryIsotopeLibrary | Create complementary isotope (Arg, Lys H/L) spectral library |
| createLibrarySpectrum | Parse spectrum framgment match information listed in MaxQuant... |
| createSpectralLibrary | Create Spectral Library |
| digestProteome | Get peptide candidates per protein |
| getCMDLineOptions | Define and User Specified Command Line Options |
| getEmpiricalIRT | Add iRT metric to data.frame |
| getFragmentSequence | Get Fragment Sub Sequnece |
| getIRTModel | Get linear model predicting iRT as a function retention time... |
| getPeptides | Get Mz Shift of complementary peptide/fragment ion |
| getPTMColors | assign colors to ptms |
| getSearchedModifications | Get list of variable modifiections condsidered by MaxQuant |
| getUserOptions | check and return User Specified Command Line Options |
| parseMaxQuantMSMS | Parse MaxQuant msms.txt |
| parseRange | Parse range in format 2:4 and return integer vector. Inthis... |
| parseTargetsFile | Parse list of target peptides/proteins |
| plotIRTCalibration | Plot IRT calibration curve |
| proteotypicPeptideExport | # Export top X peptide per protein (ordered by... |
| skylineExport | Write skyline compatible xls file |
| spectroDiveExport | Write SpectroDive compatible xls file |
| spectronautExport | Write Spectronaut compatible xls file |
