MsChromList-class: Class to handle extracted ion chromatograms

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

Description

This class is a container for one or several XIC from MsData object(s).

Usage

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

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

## S4 method for signature 'MsChromList,numeric,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MsChromList,logical,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MsChromList'
msPlot(object, type = c("TIC", "BPC"),
  collapse = FALSE, ...)

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

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

Arguments

object	An MsChromList object
x	An MsChromList object
type	Which type of plots should be plotted
collapse	Should 'BPC' and 'TIC' be overlayed or on separate plots, TRUE means overlayed.
x	An MsChromList object

Value

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

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

• [: Subset an MsList object

• [: Subset an MsList object

• msPlot: Create a plot

• msInfo: Get information about the chromatograms

• msData: Get the chromatogram data

Slots

connections

A list of MsConnections

info

A data.frame with information on the contained XIC

data

A matrix containing the raw data pertaining to the XIC

mapping

A matrix with the mapping of XIC to the rows in the @data matrix

See Also

Other MSsary-classees: MsIonList-class, msData,MsIonList-method, msInfo,MsIonList-method, msPlot,MsIonList-method, names,MsIonList-method, show,MsIonList-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.