MassSpectra {tofsims} | R Documentation

## Class `MassSpectra`

### Description

Class `MassSpectra` is the main data container in the tofsims package as it contains the individual mass spectra.

`MassSpectra` is also the call to class constructor. It is used for importing high-resolution mass spectra from raw data.

### Usage

    MassSpectra(select = c("ulvacraw", "iontofgrd", "dummy"), analysisName, ...)

    MassSpectra(select = c("ulvacraw", "iontofgrd", "dummy"), analysisName, ...)

### Arguments

`select` | `character`, 'ulvacraw', 'iontofgrd', 'dummy'
`analysisName` | `character`, the (file)name of the dataset
`...` | additional args

### Details

Class `MassSpectra` is the main data container of the `tofsims` package, containing the individual mass spectra in the slot `nz`. Additional metadata about the analysis can be found in the slots `analysisName` and `instrument`. Values for slope and intercept of the linear mass calibration equation are stored in the slot `calibration`. The M/z values can be found in `mz`. `calibration` allows calculating from M/z values back to times-of-flight. The slot `calibPoints` is used to recalibrate the dataset. It contains a data.frame with the columns `mz` and `TOF`. The slot `analysis` of type `list`, is used as a container for data analysis objects. Typically, object of the class `MassSpectra` are constructed during data import using the user constructor function with the same name as the class, `MassSpectra`.

`MassSpectra` is also the call to class constructor. It is used for importing high-resolution mass spectra from raw data.

### Value

object of class MassSpectra

### Slots

`analysisName`

  character vector with the import filename

`instrument`

  character vector type of instrument used in the experiment

`calibration`

  data frame for numerics slope and intercept of the mass calibration

`calibPoints`

  data frame for time of flight to maass to charge calibration

`nz`

  matrix with rows of ion counts and columns as toftimes or mass to charge ratios

`mz`

  vector same length as columns in `nz` for mass to charge values

### Author(s)

Lorenz Gerber <lorenz.gerber@slu.se>

### Examples

    ## Not run:
    ## access rawdata in tofsims package
    library(tofsimsData)
    importFile<-system.file("rawdata", "trift_test_001.RAW", package = "tofsimsData")
    MassSpectra('ulvacraw', importFile)

    ## End(Not run)
    ## create dummy MassSpectra object
    MassSpectra('dummy')

[Package tofsims version 1.8.0 Index]