Class xcmsRaw, a class for handling raw data

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)

% \item{\code{msnPeakCount}:}{msnPeakCount is equal to scan length} OBSOLETED

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

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

See also

xcmsRaw, subset-xcmsRaw for subsetting by spectra.