xcms-conv: Conversion to XCMS objects
In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

getXCMSSet

R Documentation

Conversion to XCMS objects

Description

Converts a features or featureGroups object to an xcmsSet or XCMSnExp object.

Usage

getXCMSSet(obj, verbose = TRUE, ...)

getXCMSnExp(obj, verbose = TRUE, ...)

## S4 method for signature 'features'
getXCMSSet(obj, verbose, loadRawData)

## S4 method for signature 'featuresXCMS'
getXCMSSet(obj, verbose = TRUE, ...)

## S4 method for signature 'featureGroups'
getXCMSSet(obj, verbose, loadRawData)

## S4 method for signature 'featureGroupsXCMS'
getXCMSSet(obj, verbose, loadRawData)

## S4 method for signature 'featuresSet'
getXCMSSet(obj, ..., set)

## S4 method for signature 'featureGroupsSet'
getXCMSSet(obj, ..., set)

## S4 method for signature 'features'
getXCMSnExp(obj, verbose, loadRawData)

## S4 method for signature 'featuresXCMS3'
getXCMSnExp(obj, verbose = TRUE, ...)

## S4 method for signature 'featureGroups'
getXCMSnExp(obj, verbose, loadRawData)

## S4 method for signature 'featureGroupsXCMS3'
getXCMSnExp(obj, verbose, loadRawData)

## S4 method for signature 'featuresSet'
getXCMSnExp(obj, ..., set)

## S4 method for signature 'featureGroupsSet'
getXCMSnExp(obj, ..., set)

Arguments

`obj`	The object that should be converted.
`verbose`	If `FALSE` then no text output is shown.
`...`	\setsWF Further arguments passed to non-sets method. Otherwise ignored.
`loadRawData`	Set to `TRUE` if analyses are available as `mzXML` or `mzML` files. Otherwise MS data is not loaded, and some dummy data (e.g. file paths) is used in the returned object.
`set`	\setsWF The name of the set to be exported.