meta.export {immunoClust} | R Documentation

## immunoClust Meta-clustering Results Export

### Description

Thess functions collect the output of the `meta.process` and extracts the event numbers, relative frequencies or mean fluorescence intensities for each meta-cluster and cell-clustering experiment in a numeric table.

### Usage

    meta.numEvents(meta, out.all=TRUE, out.removed=FALSE,  out.unclassified=TRUE)
    meta.relEvents(meta, out.all=TRUE)

    meta.parMFI(meta, par, out.all=TRUE)

    meta.numClusters(meta, out.all=TRUE)

    meta.freqTable(meta)

    meta.relEvents2(meta, major=1:5, out.all=TRUE)

    meta.relEvents3(meta, major=1:5, out.all=TRUE)

    meta.majorEvents(meta, major=1:6, out.events=TRUE)

### Arguments

`meta` | The list-object returned by the function meta.process.
`par` | An integer index to the specific parameter.
`out.all` | A numeric indicator whether the event numbers of all hierarchical gating levels are obtained or only the meta-clusters themselves.
`out.removed` | A numeric indcator whether the number of removed events, which are not used for clustering are exported.
`out.unclassified` | A numeric indicator whether the event numbers of the hierarchical gating levels or all meta-clusters are exported.
`out.events` | Switch between cell event numbers and relative cell frequencies.
`major` | A numeric array indication the major scatter regions which were used as total events.

### Value

A numberic matrix with

numEvents

  the number of cell events

relEvents

  relative frequencies, i.e. the number of cell events per total meeasured events

parMFI

  mean fluorecence intensities in one parameter, i.e. the meta-cluster centers in asinh-tranformed scale

numClusters

  the number of cell clusters

freqTable

  relative frequencies with respect to all gating hierarchie levels

relEvents2

  prelimary function; as relEvents but is restricted to the events in the given major scatter regions.

relEvents3

  prelimary function; union of relEvents and relEvents2

majorEvents

  the number of cell events for the major regions only

in each meta-cluster (and gating hierarchy level) for each cell-clustering experiment.

### Author(s)

Till Sörensen till-antoni.soerensen@charite.de

### References

Sörensen, T., Baumgart, S., Durek, P., Grützkau, A. and Häupl, T. immunoClust - an automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets. Cytometry A (submitted).

### See Also

`meta.process`

### Examples

    data(dat.exp)
    meta <- meta.process(dat.exp)
    tbl <- meta.numEvents(meta)

[Package immunoClust version 1.12.0 Index]