xcmsRaw-class {xcms} | R Documentation |
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.
env
: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
:scantime
:scanindex
:mz
and intensity
variables (note that index
values are based off a 0 initial position instead of 1)
profmethod
:mzrange
:gradient
:time
, containing the time point
for interpolation and successive columns representing solvent
fractions at each point
msmsinfo
:parent
, containing parent ion
m/z and sucessive columns representing additional information
about fragmentation (energy, etc.)
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
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
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")
: 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
signature(object = "xcmsRaw")
: sort the data points
by increasing m/z for each scan
No notes yet.
Colin A. Smith, csmith@scripps.edu
A parallel effort in metabolite profiling data sharing: http://metlin.scripps.edu/