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]