| baselineCorrect.pSet | Substract baseline intensities | 
| baseline_correct | Substract baseline intensities | 
| clade | peptideSet methods | 
| clade-method | peptideSet methods | 
| clade-methods | peptideSet methods | 
| create_db | Create a peptide collection | 
| end-method | peptideSet methods | 
| featureID | peptideSet methods | 
| featureID-method | peptideSet methods | 
| makeCalls | Make antibody binding positivity calls | 
| makePeptideSet | peptideSet constructor | 
| NormalizeArray | Normalize tiling array data using sequence information | 
| normalizeArray | Normalize tiling array data using sequence information | 
| peptide | peptideSet methods | 
| peptide-method | peptideSet methods | 
| peptide<- | peptideSet methods | 
| peptide<--method | peptideSet methods | 
| peptideSet | peptideSet class | 
| peptideSet-class | peptideSet class | 
| peptideSet-methods | peptideSet methods | 
| pepZscore | peptideSet methods | 
| pepZscore-method | peptideSet methods | 
| pepZscore<- | peptideSet methods | 
| pepZscore<--method | peptideSet methods | 
| plotArrayImage | Plot microarray images | 
| plotArrayResiduals | Plot microarray images | 
| position | peptideSet methods | 
| position-method | peptideSet methods | 
| ranges-method | peptideSet methods | 
| ranges<--method | peptideSet methods | 
| restab | Result table | 
| shinyPepStat | Launch the pepStat Shiny Application | 
| show-method | peptideSet methods | 
| slidingMean | Data smoothing for peptide microarray. | 
| start-method | peptideSet methods | 
| subset-method | peptideSet methods | 
| summarizePeptides | Add information to a peptideSet and summarize peptides | 
| summary-method | peptideSet methods | 
| values-method | peptideSet methods | 
| width-method | peptideSet methods | 
| [-method | peptideSet methods |