ruleSet-class: Class 'ruleSet'

In CAMERA: Collection of annotation related methods for mass spectrometry data

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)

CAMERA documentation built on Nov. 8, 2020, 4:59 p.m.