immunoClust-object {immunoClust} | R Documentation

## immunoClust-Object

### Description

The `immunoClust` object contains the clustering results in the immunoClust-pipeline as obtained by `cell.process` or `meta.process`.

### Usage

    ## S4 method for signature 'immunoClust'
    summary(object)
    ## S4 method for signature 'immunoClust'
    show(object)

### Arguments

`object` | An object of class `immunoClust` as returned by the `cell.process` or `meta.process` functions of the immunoClust-pipeline.

### Value

An object of class `immunoClust` has the following slots:

`expName` | The name of the clustering experiment.
`fcsName` | The path of the clustered FCS-file.
`parameters` | The parameters used for clustering.
`removed.below` | Number of observations removed from below.
`removed.above` | Number of observations removed from above.
`trans.a` | The P-dimensional vector of the scaling factors for the asinh-transformation of each used parameter. A scaling factor of 0 indicates that a parameter is not transformed.
`trans.b` | The P-dimensional vector of the translations for the asinh-transformation of each used parameter.
`trans.decade` | experimental; should be -1.
`trans.scale` | experimental; should be 1.0.
`K` | The number of clusters.
`N` | The number of observations.
`P` | The number of used parameters.
`w` | The K-dimensional vector of the mixture proportions.
`mu` | The K x P-dimensional matrix of the K estimated cluster means.
`sigma` | The K x P x P-dimensional matrix of the K estimated cluster covariance matrices.
`z` | The K x N-dimensional matrix containing the posterior probabilities of cluster membership.
`label` | The N-dimensional vector containing the maximum a posteriori estimator for cluster membership.
`logLike` | A vector of length 3 containing the BIC, ICL and the classification likelihood without penalty of the fitted model.
`BIC` | The Bayesian Information Criterion for the fitted mixture model.
`ICL` | The Integrate Classification Likelihood for the fitted model.
`history` | experimental; unused so far.
`state` | experimental; unused so far.

### 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 (accepted).

### See Also

`cell.process`, `meta.process`

### Examples

    data(dat.exp)
    summary(dat.exp[[1]])

[Package immunoClust version 1.22.0 Index]