plotAvgMS2: Plot averaged MS2 spectrum for a selected m/z or scans

In ohgane/ShotgunLipidomicsR: Utility Functions for Analysis/Visualization of ShotgunLipidomics Data.

Description

From xcmsRaw object, this function allows plotting MS2 spectrum for a selected m/z or selected scans, with peak labels and PrecursorMz line. Additionally, common noise peaks can be excluded from the peak labels.

Usage

plotAvgMS2(xcmsraw, mz = NULL, scanNum = NULL, mzabs = 0.1, digits = 4,
  mzrange = NULL, halfWindowSize = NULL, SNR = 5, top = 10,
  noisePeaks = NULL, ...)

Arguments

xcmsraw	xcmsRaw object
mz	Precursor m/z value to plot (default NULL). Either one of the mz or scanNum is used.
scanNum	Scan numbers to plot (default NULL). A numeric vector.
mzabs	Tolerance for scan selection in absolute m/z values.
digits	Digits for peak label.
mzrange	m/z range to plot.
halfWindowSize	See MALDIquant::labelPeaks() for detail.
SNR	See MALDIquant::labelPeaks() for detail.
top	The number of peaks to label (default 10).
noisePeaks	A numeric vector. Peaks that should not be labeled.

Value

Invisibly (only when assigned to a variable) returns averaged spectrum as a data frame. If no MS/MS spectrum is found for the precursor m/z or scan numbers, NULL is returned.

ohgane/ShotgunLipidomicsR documentation built on May 24, 2019, 11:55 a.m.