| Function | Description |
| cals-methods | Similarity by user defined function |
| calssim | Similarity function for comparison of two peak-lists. |
| fbinary-methods | Binary measures for pairwise peak-list comparison |
| fcor-methods | Similarity measures for peak-list comparison |
| fdist-methods | Euclidean or Manhattan distance for peak-list comparison |
| fintersect-methods | Intersection of two vectors, Massvectors |
| finterS-methods | Intersection of two vectors, Massvectors |
| fis.element-methods | Performs *set* membership on two Massvectors |
| fmatchall-methods | Index of matching and not-matching peaks |
| fmatch-methods | Index of matching peaks |
| fsetdiff-methods | difference |
| fsetequal-methods | Performs *set* equality on two Massvectors |
| funion-methods | Union of two Massvectors |
| gamasses-methods | Determines clusters of masses in an Massvector |
| List-class | Class "List" |
| listdist-methods | compute object of class "dist" from list. |
| Massvector-class | Class "Massvector" |
| Massvectorlist-class | Class "Massvectorlist" |
| Mlist-class | Class "Mlist" |
| nrmatch-methods | Number of matching peaks |
| numeric-class | Class "numeric" |
| pldata | 18 Peak-lists |
| pmf.binary | Transformation and other factors of the pairwise peak-lists Comparsion Process |