xcmsRaw-class {xcms} | R Documentation

## Class xcmsRaw, a class for handling raw data

### Description

This class handles processing and visualization of the raw data from a single LC/MS or GS/MS run. It includes methods for producing a standard suite of plots including individual spectra, multi-scan average spectra, TIC, and EIC. It will also produce a feature list of significant peaks using matched filtration.

### Objects from the Class

Objects can be created with the `xcmsRaw` constructor which reads data from a NetCDF file into a new object.

### Slots

`env`:
  environment with three variables: `mz` - concatenated m/z values for all scans, `intensity` - corresponding signal intensity for each m/z value, and `profile` - matrix represention of the intensity values with columns representing scans and rows representing equally spaced m/z values
`tic`:
  numeric vector with total ion count (intensity) for each scan
`scantime`:
  numeric vector with acquisition time (in seconds) for each scan
`scanindex`:
  integer vector with starting positions of each scan in the `mz` and `intensity` variables (note that index values are based off a 0 initial position instead of 1)
`profmethod`:
  characer value with name of method used for generating the profile matrix
`mzrange`:
  numeric vector of length 2 with minimum and maximum m/z values represented in the profile matrix
`gradient`:
  matrix with first row, `time`, containing the time point for interpolation and successive columns representing solvent fractions at each point
`msmsinfo`:
  matrix with first row, `parent`, containing parent ion m/z and sucessive columns representing additional information about fragmentation (energy, etc.)

### Methods

findPeaks
  `signature(object = "xcmsRaw")`: feature detection using matched filtration in the chromatographic time domain
getEIC
  `signature(object = "xcmsRaw")`: get extracted ion chromatograms in specified m/z ranges
getPeaks
  `signature(object = "xcmsRaw")`: get data for peaks in specified m/z and time ranges
getScan
  `signature(object = "xcmsRaw")`: get m/z and intensity values for a single mass scan
getSpec
  `signature(object = "xcmsRaw")`: get average m/z and intensity values for multiple mass scans
image
  `signature(x = "xcmsRaw")`: get data for peaks in specified m/z and time ranges
plotChrom
  `signature(object = "xcmsRaw")`: plot a chromatogram from profile data
plotRaw
  `signature(object = "xcmsRaw")`: plot locations of raw intensity data points
plotScan
  `signature(object = "xcmsRaw")`: plot a mass spectrum of an individual scan from the raw data
plotSpec
  `signature(object = "xcmsRaw")`: plot a mass spectrum from profile data
plotSurf
  `signature(object = "xcmsRaw")`: experimental method for plotting 3D surface of profile data with `rgl`.
plotTIC
  `signature(object = "xcmsRaw")`: plot total ion count chromatogram
profMedFilt
  `signature(object = "xcmsRaw")`: median filter profile data in time and m/z dimensions
profMethod<-
  `signature(object = "xcmsRaw")`: change the method of generating the `profile` matrix
profMethod
  `signature(object = "xcmsRaw")`: get the method of generating the `profile` matrix
profMz
  `signature(object = "xcmsRaw")`: get vector of m/z values for each row of the `profile` matrix
profRange
  `signature(object = "xcmsRaw")`: interpret flexible ways of specifying subsets of the `profile` matrix
profStep<-
  `signature(object = "xcmsRaw")`: change the m/z step used for generating the `profile` matrix
profStep
  `signature(object = "xcmsRaw")`: get the m/z step used for generating the `profile` matrix
revMz
  `signature(object = "xcmsRaw")`: reverse the order of the data points for each scan
sortMz
  `signature(object = "xcmsRaw")`: sort the data points by increasing m/z for each scan

### Note

No notes yet.

### Author(s)

Colin A. Smith, csmith@scripps.edu

### References

A parallel effort in metabolite profiling data sharing: http://metlin.scripps.edu/

### See Also

`xcmsRaw`

[Package xcms version 1.6.1 Index]