convert: Methods for conversion between flowCore and flowWorkspace...

In flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Description

These methods perform conversions between flowWorkspace classes (cytoframe/cytoset) and flowCore classes (flowFrame/flowSet) as well as between single-sample and aggregated classes (e.g. between cytoset and a list of cytoframes)

Usage

cytoframe_to_flowFrame(cf)

flowFrame_to_cytoframe(fr, ...)

cytoset_to_flowSet(cs)

flowSet_to_cytoset(
  fs,
  path = tempfile(),
  backend = get_default_backend(),
  tmp = tempfile()
)

cytoset_to_list(cs)

Arguments

cf	cytoframe object
fr	flowframe
...	arguments passed to 'load_cytoframe_from_fcs' call
cs	cytoset
fs	flowSet or ncdfFlowSet
path	the h5 path for cytoset
tmp	the temp folder when the temporary files are written to during conversion by default, it is system temp path. And it can be changed to the customized location when there is not enough space at system path.

Details

The first set of methods consist of a pair of methods to coerce a cytoframe to or from a flowFrame and another pair to coerce a cytoset to or from a flowSet.

The conversion between the two sets of data container classes mostly entails a conversion of the back-end representation of the data. cytoframe and cytoset objects contain flowFrame and flowSet objects respectively, so coercion of a cytoframe to flowFrame entails moving the data from the 'C'-level data structure to the corresponding exprs, description, and parameters slots. Coercion of a flowFrame to a cytoframe entails creation of the 'C'-level data structure from the flowFrame slots. The names of each of the methods are pretty self-explanatory.

The second set of methods perform disaggregation of data objects that represent multiple samples in to lists of data objects that represent a single sample. The opposite direction is handled by the constructors for the aggregate data classes.

Methods

cytoframe_to_flowFrame(object = "cytoframe")

Returns a flowFrame object coerced from a cytoframe object.

flowFrame_to_cytoframe(object = "flowFrame")

Returns a cytoframe object coerced from a flowFrame object.

cytoset_to_flowSet(object = "cytoset")

Returns a flowSet object coerced from a cytoset object.

flowSet_to_cytoset(object = "flowSet")

Returns a cytoset object coerced from a flowSet object.

flowSet_to_list(object = "flowSet")

Returns a list of cytoframe objects with names provided by the sampleNames of the original cytoset

flowSet(object = "list)

Constructs a cytoset object from a list of cytoframe objects. See documentation for cytoset

cytoset_to_list(object = "cytoset")

Returns a list of cytoframe objects with names provided by the sampleNames of the original cytoset

cytoset(object = "list)

Constructs a cytoset object from a list of cytoframe objects. See documentation for flowSet

See Also

merge_list_to_gs

Examples

library(flowCore)
data("GvHD")
fs <- GvHD[1]
cs <- flowSet_to_cytoset(fs)
cf <- cs[[1, returnType="cytoframe"]]
ff <- cytoframe_to_flowFrame(cf)

flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.