ruleSet {CAMERA} | R Documentation

## Class `ruleSet`

### Description

The class `ruleSet` is used to read lists of ions, adducts and neutral losses, and compile the dynamic ruleSet from those. This makes it possible to modify the default rules for certain analytical settings.

### Slots

`ionlistfile`:

  File of known charged ions, an example is found in CAMERA/lists/ions.csv .

`neutrallossfile`:

  File of known neutral losses, an example is found in CAMERA/lists/neutralloss.csv.

`neutraladditionfile`:

  File of known adducts, an example is found in CAMERA/lists/lists/neutraladdition.csv .

`ionlist`:

  Known charged ions.

`neutralloss`:

  Known neutral losses.

`neutraladdition`:

  Known adducts.

`maxcharge`:

  .

`mol` :

  .

`nion` :

  .

`nnloss` :

  .

`nnadd` :

  .

`nh` :

  .

`polarity` :

  Polarity of the ruleSet.

`rules`:

  data.frame of resulting mass differences, this is the dynamic ruleSet.

`lib.loc`

  Path to local R library

### Extends

Class `"Versioned"`, directly.

### Methods

Methods implemented for `ruleSet`

setDefaultLists

  `signature(object = "ruleSet")`: Set filenames for the lists shipped with CAMERA.

readLists

  `signature(object = "ruleSet")`: Read and parse the lists from the files.

setDefaultParams

  `signature(object = "ruleSet")`: Set the default parameters for rule generation.

setParams

  `signature(object = "ruleSet")`: Set the parameters for rule generation.

generateRules

  `signature(object = "ruleSet")`: Create the rules in `ruleSet@rules` .

### Author(s)

Steffen Neumann and Carsten Kuhl

### Examples

            r <- new("ruleSet");
            r2 <- setDefaultLists(r) ;
            r3 <- readLists(r2) ;
            r4 <- setDefaultParams(r3) ;
            r5 <- generateRules(r4)
            dim(r5@rules)

[Package CAMERA version 1.38.1 Index]