getPeaksAvgMS1: A function to pick peaks from an averaged MS1 spectrum from a...

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

Description

This function accepts xcmsRaw object with MS/MS data (direct infusion, data-dependent acquisition) and return top N peaks. Correspond to plotAvgMS1.

Usage

getPeaksAvgMS1(xcmsraw, scans = NULL, mzrange = NULL, ylim = NULL,
  ad.lab.mzrange = NA, ad.top = 3, top = 12, halfWindowSize = NULL,
  SNR = 50, digits = 4, ...)

Arguments

xcmsraw	xcmsRaw object.
scans	A numeric vector of scan indexes. If provided, only the indicated scans are averaged and plotted.
mzrange	m/z range to plot.
ylim	Y axis range to plot.
ad.top	The number of additional peak labels.
top	The number of peak labels.
halfWindowSize	See MALDIquant::labelPeaks() for detail.
SNR	See MALDIquant::labelPeaks() for detail.
digits	Digits for peak labels.
ad.lab.	mzrange m/z range to add additional peak labels.

Value

Top N peaks as a data frame.

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