MsPeakList-class: Class to handle detected peaks

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

Description

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

Usage

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

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

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

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

## S4 method for signature 'MsPeakList'
msPlot(object, type = "2d", collapse = length(object)
  > 12, simple = FALSE, precursor = !simple, mzscatter = !simple,
  context = !simple, ...)

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

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

Arguments

object	An MsPeakList object
x	An MsPeakList object

Value

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

• msPlot: Create a plot

• 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 peaks

data

A matrix containing the raw data pertaining to the peaks

mapping

A matrix with the mapping of peaks 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; 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.