MSsliceList-class: List of MSslice objects

In jotsetung/xcmsExtensions: Extensions to the xcms package

Description

The MSsliceList allows to group several MSslice objects. Each of the MSslice objects is supposed to define a different slice of the MS data (defined by a m/z values and retention time range) and to contain the intensity values for the slice across several samples. The MSsliceList object can then contain the data of several different such slices. For example, an MSslice object could contain the intensity values for a peak (defined by its mz and rt range) across all samples of an experiment (i.e. an xcmsSet object). The MSsliceList could then contain the values for several or all peaks identified in an experiment.

Usage

## S4 method for signature 'MSsliceList'
intrange(object)

## S4 method for signature 'MSsliceList'
intranges(object)

## S4 method for signature 'MSsliceList'
length(x)

MSsliceList(...)

## S4 method for signature 'MSsliceList'
mzrange(object)

## S4 method for signature 'MSsliceList'
mzranges(object)

## S4 method for signature 'MSsliceList'
rtrange(object)

## S4 method for signature 'MSsliceList'
rtranges(object)

## S4 method for signature 'MSsliceList'
slices(object)

## S4 replacement method for signature 'MSsliceList'
slices(object) <- value

Arguments

(in alphabetic order)

object	An MSsliceList object.
x	For length: an MSsliceList object.
value	For slices: a list of MSslice objects.
...	For MSsliceList: MSslice objects for the MSsliceList object. Ignored for all other methods.

Value

Refer to the method and function description above for detailed information on the returned result object.

Objects of the class

MSsliceList objects can be created by the constructor function MSsliceList but by default they are supposed to be returned by the msSlice method for xcmsSet objects with mzrange and rtrange parameters being matrices specifying different slices of data.

Slots

slices

A list of MSslice objects.

Constructors and alike

MSsliceList

Constructor method to create a new MSsliceList instance accepting either a list of MSslice objects or individual MSslice objects.

msSlice

If the provided parameters mzrange and rtrange define multiple slices, the method returns a MSsliceList object from an xcmsRaw or xcmsSet object. See the help of msSlice for more information.

Accessing and sub-setting

intrange

Get the range of the intensity value ranges of the individual slices within the object.

intranges

Returns a list of the intensity range for each individual slice within the object.

length

Get the length of the object, i.e. the number of MSslice objects stored within the object.

mzrange

Get the range of m/z value ranges of the individual slices within the object.

mzrange

Returns a list of the m/z value ranges of the individual slices within the object.

object[i]

Subsets the MSsliceList object object and returns a MSsliceList with only the elements selected by i.

object[[i]]

Extract a single MSslice object from the MSsliceList.

rtrange

Get the range of retention time ranges of the slices within the object.

rtranges

Returns a list of the retention time ranges of the individual slices within the object.

slices, slices<-

Getter and setter method for the slices slot. Returns the list of MSslice objects.

Author(s)

Johannes Rainer.

See Also

xcmsSet, xcmsRaw, MSdata, MSslice

Examples

## Load the faahKO package with the test data for the xcms package.
library(faahKO)
xset <- faahko

## Define several data sub-sets and extract the corresponding values from
## the xcmsSet object. This will extract the intensity values of the
## defined slices from each individual sample.
rtr <- rbind(c(2600, 2670),
             c(2900, 2920)
             )
mzr <- rbind(c(300, 400),
             c(401, 402)
             )
msl <- msSlice(xset, rtrange=rtr, mzrange=mzr)
msl

## Get the number of slices
length(msl)

## Get the mz, rt and intensity range. This corresponds to the range of
## ranges of the individual slices across all samples.
mzrange(msl)
rtrange(msl)
intrange(msl)

## Get the ranges for each individual slice
mzranges(msl)
rtranges(msl)
intranges(msl)

## Sub-set the MSsliceList object.
msl[2]

## Extract an individual MSslice object
msl[[2]]

jotsetung/xcmsExtensions documentation built on May 19, 2019, 9:42 p.m.