xcmsRaw-class: Class xcmsRaw, a class for handling raw data

In benjiec/xcms: LC/MS and GC/MS Data Analysis

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:

acquisitionNum

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

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:

profparam

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

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

stitch

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

Note

No notes yet.

Author(s)

Colin A. Smith, [e-mail]

References

A parallel effort in metabolite profiling data sharing: http://metlin.scripps.edu/

See Also

xcmsRaw

benjiec/xcms documentation built on May 12, 2019, 11:57 a.m.