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.
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]])
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(immunoClust)
Loading required package: grid
Loading required package: lattice
Loading required package: flowCore
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/immunoClust/immunoClust.object.Rd_%03d_medium.png", width=480, height=480)
> ### Name: immunoClust-object
> ### Title: immunoClust-Object
> ### Aliases: immunoClust.object immunoClust-class summary
> ### summary,immunoClust-method summary.immunoClust show
> ### show,immunoClust-method show.immunoClust
> ### Keywords: print
>
> ### ** Examples
>
> data(dat.exp)
> summary(dat.exp[[1]])
** Experiment Information **
Experiment name: 12543
Data Filename: fcs/12543.fcs
Parameters: FSC-A SSC-A FITC-A PE-A APC-A APC-Cy7-A Pacific Blue-A
Description: FCS SSC CD14 CD19 CD15 CD4 CD3
** Data Information **
Number of observations: 10000
Number of parameters: 7
Removed from above: 318 (3.18%)
Removed from below: 0 (0%)
** Transformation Information **
htrans-A: 0.000000 0.000000 0.007202 0.004932 0.008136 0.015128 0.023041
htrans-B: 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
htrans-decade: -1
** Clustering Summary **
Number of clusters: 13
Cluster Proportion Observations
1 0.037166 366
2 0.054083 518
3 0.001495 14
4 0.005117 50
5 0.040246 389
6 0.035741 344
7 0.015130 151
8 0.007298 71
9 0.114354 1107
10 0.282377 2558
11 0.007320 70
12 0.014736 143
13 0.384937 3901
Min. 0.001495 14
Max. 0.384937 3901
** Information Criteria **
Log likelihood: -254765.8 -256024.9 -174699.5
BIC: -254765.8
ICL: -256024.9
>
>
>
>
>
> dev.off()
null device
1
>