ProcessHistory-class {xcms} | R Documentation

## Tracking data processing

### Description

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 signature 'ProcessHistory'
    show(object)

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

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

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

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

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

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

    ## S4 method for signature '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(s)

Johannes Rainer

[Package xcms version 3.9.1 Index]