convert {flowWorkspace} | R Documentation

## Methods for conversion between flowCore and flowWorkspace data classes

### 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 `cytoframe`s)

### 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)

[Package flowWorkspace version 4.4.0 Index]