MsScanList-class: Class to handle specific scans

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

Description

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

Usage

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

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

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

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

## S4 method for signature 'MsScanList'
scanMode(object)

## S4 method for signature 'MsScanList'
msPlot(object, simple = FALSE, parent = !simple,
  precursor = !simple, peaks = !simple, masses = ifelse(simple, 0, 10),
  context = !simple, tolerance = 20, ...)

## S4 method for signature 'MsScanList'
nextScan(object, sameLevel = TRUE)

## S4 method for signature 'MsScanList'
previousScan(object, sameLevel = TRUE)

## S4 method for signature 'MsScanList'
parent(object)

## S4 method for signature 'MsScanList'
children(object)

## S4 method for signature 'MsScanList'
siblings(object)

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

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

Arguments

object	An MsScanList object
x	An MsScanList object

Value

nextScan: An MsScanList object with the next scan

previousScan: An MsScanList object with the previous scan

parent: An MsScanList object with the parent scan

children: A list of MsScanList objects with the children scans

siblings: A list of MsScanList objects with the sibling scans

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

msData: A list of matrices with m/z values in the first column and intensity in the second

Methods (by generic)

• show: Short summary of object

• names: Get the names of the scans

• [: Subset an MsList object

• [: Subset an MsList object

• scanMode: Get the mode of the scan

• msPlot: Create a plot

• nextScan: Get the next scan

• previousScan: Get previous scan

• parent: Get the scan containing the parent ion for this scan

• children: Get fragmentation scans from this scan

• siblings: Get all scans with the same parent

• msInfo: Get information about the scan

• msData: Get the scan data

Slots

connections

A list of MsConnections

info

A data.frame with information on the contained scans

data

A matrix containing the raw data pertaining to the scans

mapping

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

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; 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

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