Description Objects from the Class Slots Methods Author(s) See Also
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 can be created with the xcmsRaw
constructor
which reads data from a NetCDF file into a new object.
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.
signature(object = "xcmsRaw")
: feature detection using
matched filtration in the chromatographic time domain
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).
signature(object = "xcmsRaw")
: get data for peaks in
specified m/z and time ranges
signature(object = "xcmsRaw")
: get m/z and intensity
values for a single mass scan
signature(object = "xcmsRaw")
: get average m/z and
intensity values for multiple mass scans
signature(x = "xcmsRaw")
: get data for peaks in
specified m/z and time ranges
Create an image of the raw (profile) data m/z against retention time, with the intensity color coded.
Getter method for the mslevel
slot.
signature(object = "xcmsRaw")
: plot a chromatogram
from profile data
signature(object = "xcmsRaw")
: plot locations of raw
intensity data points
signature(object = "xcmsRaw")
: plot a mass spectrum
of an individual scan from the raw data
signature(object = "xcmsRaw")
: plot a mass spectrum
from profile data
signature(object = "xcmsRaw")
: experimental method for
plotting 3D surface of profile data with rgl
.
signature(object = "xcmsRaw")
: plot total ion count
chromatogram
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.
signature(object = "xcmsRaw")
: median filter profile
data in time and m/z dimensions
signature(object = "xcmsRaw")
: change the method of
generating the profile
matrix
signature(object = "xcmsRaw")
: get the method of
generating the profile
matrix
signature(object = "xcmsRaw")
: get vector of m/z values
for each row of the profile
matrix
signature(object = "xcmsRaw")
: interpret flexible ways
of specifying subsets of the profile
matrix
signature(object = "xcmsRaw")
: change the m/z step
used for generating the profile
matrix
signature(object = "xcmsRaw")
: get the m/z step used
for generating the profile
matrix
signature(object = "xcmsRaw")
: reverse the order of the
data points for each scan
Getter method for the scanrange
slot. See slot description
above for more information.
signature(object = "xcmsRaw")
: sort the data points
by increasing m/z for each scan
signature(object = "xcmsRaw")
: Raw data correction for
lock mass calibration gaps.
Colin A. Smith, csmith@scripps.edu, Johannes Rainer johannes.rainer@eurac.edu
xcmsRaw
, subset-xcmsRaw
for subsetting by spectra.
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