Tracking data processing — ProcessHistory-class • xcms

Objects of the type ProcessHistory allow to keep track of any data processing step in an metabolomics experiment. They are created by the data processing methods, such as findChromPeaks and added to the corresponding results objects. Thus, usually, users don't need to create them.

The XProcessHistory extends the ProcessHistory by adding a slot param that allows to store the actual parameter class of the processing step.

processParam, processParam<-: get or set the parameter class from an XProcessHistory object.

msLevel: returns the MS level on which a certain analysis has been performed, or NA if not defined.

The processType method returns a character specifying the processing step type.

The processDate extracts the start date of the processing step.

The processInfo extracts optional additional information on the processing step.

The fileIndex extracts the indices of the files on which the processing step was applied.

Usage

# S4 method for class 'ProcessHistory'
show(object)

# S4 method for class 'XProcessHistory'
show(object)

# S4 method for class 'XProcessHistory'
processParam(object)

# S4 method for class 'XProcessHistory'
msLevel(object)

# S4 method for class 'ProcessHistory'
processType(object)

# S4 method for class 'ProcessHistory'
processDate(object)

# S4 method for class 'ProcessHistory'
processInfo(object)

# S4 method for class 'ProcessHistory'
fileIndex(object)

Arguments

object: A ProcessHistory or XProcessHistory object.

Value

For processParam: a parameter object extending the Param class.

The processType method returns a character string with the processing step type.

The processDate method returns a character string with the time stamp of the processing step start.

The processInfo method returns a character string with optional additional informations.

The fileIndex method returns a integer vector with the index of the files/samples on which the processing step was applied.

Slots

type: character(1): string defining the type of the processing step. This string has to match predefined values. Use processHistoryTypes to list them.
date: character(1): date time stamp when the processing step was started.
info: character(1): optional additional information.
fileIndex: integer of length 1 or > 1 to specify on which samples of the object the processing was performed.
error: (ANY): used to store eventual calculation errors.
param: (Param): an object of type Param (e.g. CentWaveParam) specifying the settings of the processing step.
msLevel:: integer definining the MS level(s) on which the analysis was performed.

Author

Johannes Rainer