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

`acquisitionNum`:

  Numeric representing the acquisition number of the individual scans/spectra. Length of `acquisitionNum` is equal to the number of spectra/scans in the object and hence equal to the `scantime` slot. Note however that this information is only available in mzML files.

`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. The profile matrix should be extracted with the `profMat` method.

`filepath`:

  Path to the raw data file

`gradient`:

  matrix with first row, `time`, containing the time point for interpolation and successive columns representing solvent fractions at each point

`msnAcquisitionNum`:

  for each scan a unique acquisition number as reported via "spectrum id" (mzData) or "<scan num=...>" and "<scanOrigin num=...>" (mzXML)

`msnCollisionEnergy`:

  "CollisionEnergy" (mzData) or "collisionEnergy" (mzXML)

`msnLevel`:

  for each scan the "msLevel" (both mzData and mzXML)

`msnPrecursorCharge`:

  "ChargeState" (mzData) and "precursorCharge" (mzXML)

`msnPrecursorIntensity`:

  "Intensity" (mzData) or "precursorIntensity" (mzXML)

`msnPrecursorMz`:

  "MassToChargeRatio" (mzData) or "precursorMz" (mzXML)

`msnPrecursorScan`:

  "spectrumRef" (both mzData and mzXML)

`msnRt`:

  Retention time of the scan

`msnScanindex`:

  msnScanindex

`mzrange`:

  numeric vector of length 2 with minimum and maximum m/z values represented in the profile matrix

`polarity`:

  polarity

`profmethod`:

  characer value with name of method used for generating the profile matrix.

`profparam`:

  list to store additional profile matrix generation settings. Use the `profinfo` method to extract all profile matrix creation relevant information.

`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).

`scantime`:

  numeric vector with acquisition time (in seconds) for each scan.

`tic`:

  numeric vector with total ion count (intensity) for each scan

`mslevel`:

  Numeric representing the MS level that is present in MS1 slot. This slot should be accessed through its getter method `mslevel`.

`scanrange`:

  Numeric of length 2 specifying the scan range (or `NULL` for the full range). This slot should be accessed through its getter method `scanrange`. Note that the `scanrange` will always be 1 to the number of scans within the `xcmsRaw` object, which does not necessarily have to match to the scan index in the original mzML file (e.g. if the original data was sub-setted). The `acquisitionNum` information can be used to track the original position of each scan in the mzML file.

### 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. This will return the total ion chromatogram (TIC) if the m/z range corresponds to the full m/z range (i.e. sum of all signals per retention time across all m/z).

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

levelplot

  Create an image of the raw (profile) data m/z against retention time, with the intensity color coded.

mslevel

  Getter method for the `mslevel` slot.

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

profinfo

  `signature(object = "xcmsRaw")`: returns a list containing the profile generation method and step (profile m/z step size) and eventual additional parameters to the profile function.

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

scanrange

  Getter method for the `scanrange` slot. See slot description above for more information.

sortMz

  `signature(object = "xcmsRaw")`: sort the data points by increasing m/z for each scan

stitch

  `signature(object = "xcmsRaw")`: Raw data correction for lock mass calibration gaps.

findmzROI

  `signature(object = "xcmsRaw")`: internal function to identify regions of interest in the raw data as part of the first step of centWave-based peak detection.

### Author(s)

Colin A. Smith, csmith@scripps.edu, Johannes Rainer johannes.rainer@eurac.edu

### See Also

`xcmsRaw`, `subset-xcmsRaw` for subsetting by spectra.

[Package xcms version 3.16.1 Index]