R: Internal Fragment Identification from Top-Down Mass Spectrometry

# Internal Fragment Identification from Top-Down Mass Spectrometry

## Documentation for package ‘wrTopDownFrag’ version 1.0.4

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

.chargeCatchingAA | Cite Charge Catching Amino-Acids
.chColNa | Check Column Names from Matrix Or data.frame
.checkModTy | Check Modification Type
.countLET | Count Letters
.countModif | Count For All Proteins The Occurance Of Modification Types
.CtermPepCut | Make Named Character Vector Of Sequential C-Terminal Fragments
.evalIsoFra | Evaluate Selected Lines Of PepTab
.exNamesTyDeList | Reorganize List Of Peptide Fragments To Matrix
.multMatByColNa | Multiply Values Of Matrix By Its Colnames And Sum By Row
.NtermPepCut | Make Named Character Vector Of Sequential C-Terminal Fragments
.parCombinateAllAndSum | Multiprocessor Version For Full Combinatorial And Cumulative Values
.prefFragPattern | Return data.frame with pattern of perferential fragmentation sites
.singleSpecModif | Add Single Specific Modifications
.termPepCut | Make Named Character Vector Of Sequential Terminal Fragments
AAfragSettings | Settings For AA Fragmentation
addMassModif | Add Modifications To Peptide Mass
checkModTy | Check & complete mixed of variable and fixed modifications
combinateAllAndSum | Full Combinatorial And Cumulative Values
combinatIntTable | Planing For Making All Multiplicative Combinations
corInDelShift | Corrective Values For Random Sequences For In/Dels
corMutShift | Corrective Values For Random Sequences For Mutations
countChildrenParent | Identify Children/Parent Settings As a+b=c
countPotModifAAs | Make Table With Counts of Potential Modification Sites
evalIsoFragm | Evaluate Selected Lines Of PepTab (iso-mass) For Preferential Cutting Sites
fragmentSeq | Fragment Protein Or Peptide Sequence
identifFixedModif | Identify Fixed Modifications
identifVarModif | Idenitfy Variable Modifications
identifyPepFragments | Identify terminal and internal protein/peptide-fragments as matches to experimental MS-peaks
makeFragments | Make Terminal And Internal Fragments From Proteins
modifFragmTabOutput | Change fragment identification output format (for biologists)
plotFragmLoc | Plot Identified Fragments Relative To Their Location
plotMgfLike | Draw simplified (deconvoluted) spectrum of mgf type and highlight peaks with matches found to theoretical data
plotNTheor | Plot the number of theoretical random fragments
plotPrefFragPat | plot preferential fragmenation pattern Plot preferential fragmenation pattern equivalent to Fig 1b of Haverland et al 2017 (J Am Soc Mass Spectrom)
randMassByMut | Make decoy mass by full randomization
randMassByStochastic | Make Decoy Mass By Full Randomization
scoreChargeCatch | Scoring Of Charge Catching Potential For Peptides
scoreFragments | Scoring For Single Protein : Individual Components
scorePrefFrag | Identifcation and scoring of preferential cuting sites
scoreProteinFragments | Scoring Of Identifications (For Multi-Protein Queries)