MsIonList-class: Class to handle raw ion reads

In thomasp85/MSsary: LC-MS/MS analysis in R

Description

This class is a container for ion data from a slice of an MsData object. Unlike other MsList subclasses this class can only contain one slice.

Usage

## S4 method for signature 'MsIonList'
show(object)

## S4 method for signature 'MsIonList'
names(x)

## S4 method for signature 'MsIonList'
msPlot(object, type = "2d", simple = FALSE,
  precursor = !simple, peaks = !simple, ...)

## S4 method for signature 'MsIonList'
msInfo(object)

## S4 method for signature 'MsIonList'
msData(object)

Arguments

object	An MsIonList object
x	An MsIonList object
type	Which type of plots should be plotted

Value

msInfo: A data.frame with one row containing information about the ion slice

msData: A list of matrices with acquisitionNum, retentionTime, totIonCurrent and basePeakIntensity for each scan in the chromatogram

Methods (by generic)

• show: Short summary of object

• names: Get the names of the scans

• msPlot: Create a plot

• msInfo: Get information about the ion slice

• msData: Get the ion data

Slots

connections

A list of length 1 with the MsConnections object

info

A data.frame with information on the slice

data

A matrix containing the raw data pertaining to the ions in the slice

mapping

A matrix with the mapping

See Also

Other MSsary-classees: MsChromList-class, [,MsChromList,logical,missing,missing-method, [,MsChromList,numeric,missing,missing-method, msData,MsChromList-method, msInfo,MsChromList-method, msPlot,MsChromList-method, names,MsChromList-method, show,MsChromList-method; MsPeakList-class, [,MsPeakList,logical,missing,missing-method, [,MsPeakList,numeric,missing,missing-method, msData,MsPeakList-method, msInfo,MsPeakList-method, msPlot,MsPeakList-method, names,MsPeakList-method, show,MsPeakList-method; MsScanList-class, [,MsScanList,logical,missing,missing-method, [,MsScanList,numeric,missing,missing-method, children,MsScanList-method, msData,MsScanList-method, msInfo,MsScanList-method, msPlot,MsScanList-method, names,MsScanList-method, nextScan,MsScanList-method, parent,MsScanList-method, previousScan,MsScanList-method, scanMode,MsScanList-method, show,MsScanList-method, siblings,MsScanList-method

thomasp85/MSsary documentation built on May 31, 2019, 11:11 a.m.