Conversion to XCMS objects

Source: R/generics.R, R/utils-xcms.R

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Arguments

obj

The object that should be converted.

verbose

If FALSE then no text output is shown.

...

(sets workflow) 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

(sets workflow) The name of the set to be exported.

Sets workflows

In a sets workflow, unset is used to convert the feature (group) data before the object is exported.