bin,XCMSnExp-method {xcms} | R Documentation

## XCMSnExp data manipulation methods inherited from MSnbase

### Description

The methods listed on this page are `XCMSnExp` methods inherited from its parent, the `OnDiskMSnExp` class from the `MSnbase` package, that alter the raw data or are related to data subsetting. Thus calling any of these methods causes all `xcms` pre-processing results to be removed from the `XCMSnExp` object to ensure its data integrity.

`bin`: allows to bin spectra. See `bin` documentation in the `MSnbase` package for more details and examples.

`clean`: removes unused `0` intensity data points. See `clean` documentation in the `MSnbase` package for details and examples.

`filterAcquisitionNum`: filters the `XCMSnExp` object keeping only spectra with the provided acquisition numbers. See `filterAcquisitionNum` for details and examples.

The `normalize` method performs basic normalization of spectra intensities. See `normalize` documentation in the `MSnbase` package for details and examples.

The `pickPeaks` method performs peak picking. See `pickPeaks` documentation for details and examples.

The `removePeaks` method removes mass peaks (intensities) lower than a threshold. Note that these peaks refer to mass peaks, which are different to the chromatographic peaks detected and analyzed in a metabolomics experiment! See `removePeaks` documentation for details and examples.

The `smooth` method smooths spectra. See `smooth` documentation in `MSnbase` for details and examples.

### Usage

    ## S4 method for signature 'XCMSnExp'
    bin(x, binSize = 1L, msLevel.)

    ## S4 method for signature 'XCMSnExp'
    clean(object, all = FALSE, verbose = FALSE, msLevel.)

    ## S4 method for signature 'XCMSnExp'
    filterAcquisitionNum(object, n, file)

    ## S4 method for signature 'XCMSnExp'
    normalize(object, method = c("max", "sum"), ...)

    ## S4 method for signature 'XCMSnExp'
    pickPeaks(
      object,
      halfWindowSize = 3L,
      method = c("MAD", "SuperSmoother"),
      SNR = 0L,
      ...
    )

    ## S4 method for signature 'XCMSnExp'
    removePeaks(object, t = "min", verbose = FALSE, msLevel.)

    ## S4 method for signature 'XCMSnExp'
    smooth(
      x,
      method = c("SavitzkyGolay", "MovingAverage"),
      halfWindowSize = 2L,
      verbose = FALSE,
      ...
    )

### Arguments

`x` | `XCMSnExp` or `OnDiskMSnExp` object.
`binSize` | `numeric(1)` defining the size of a bin (in Dalton).
`msLevel.` | For `bin`, `clean`, `filterMsLevel`, `removePeaks`: `numeric(1)` defining the MS level(s) to which operations should be applied or to which the object should be subsetted.
`object` | `XCMSnExp` or `OnDiskMSnExp` object.
`all` | For `clean`: `logical(1)`, if `TRUE` all zeros are removed.
`verbose` | `logical(1)` whether progress information should be displayed.
`n` | For `filterAcquisitionNum`: `integer` defining the acquisition numbers of the spectra to which the data set should be sub-setted.
`file` | For `filterAcquisitionNum`: `integer` defining the file index within the object to subset the object by file.
`method` | For `normalize`: `character(1)` specifying the normalization method. See `normalize` in the `MSnbase` package for details. For `pickPeaks`: `character(1)` defining the method. See `pickPeaks` for options. For `smooth`: `character(1)` defining the method. See `smooth` in the `MSnbase` package for options and details.
`...` | Optional additional arguments.
`halfWindowSize` | For `pickPeaks` and `smooth`: `integer(1)` defining the window size for the peak picking. See `pickPeaks` and `smooth` in the `MSnbase` package for details and options.
`SNR` | For `pickPeaks`: `numeric(1)` defining the signal to noise ratio to be considered. See `pickPeaks` documentation for details.
`t` | For `removePeaks`: either a `numeric(1)` or `"min"` defining the threshold (method) to be used. See `removePeaks` for details.

### Value

For all methods: a `XCMSnExp` object.

### Author(s)

Johannes Rainer

### See Also

`XCMSnExp-filter` for methods to filter and subset `XCMSnExp` objects. `XCMSnExp` for base class documentation. `OnDiskMSnExp` for the documentation of the parent class.

[Package xcms version 3.16.1 Index]