immunoClust.object: immunoClust-Object

In immunoClust: immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

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 [e-mail]

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]])

immunoClust documentation built on Nov. 8, 2020, 5:19 p.m.