# immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

## Documentation for package ‘immunoClust’ version 1.38.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F I L M N P R S T U W

immunoClust-package | immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

## -- A --

addLevel<- | Acessors and Methods for immunoMeta Objects
addLevel<-.immunoMeta | Acessors and Methods for immunoMeta Objects
aposteriori | Generic function definitions in immunoClust
aposteriori-method | Acessors and Methods for immunoClust Objects
aposteriori-method | Acessors and Methods for immunoMeta Objects
aposteriori.immunoClust | Acessors and Methods for immunoClust Objects
aposteriori.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- B --

bhattacharyya.coeff | Bhattacharyya Distance, Coefficient and Probability
bhattacharyya.dist | Bhattacharyya Distance, Coefficient and Probability
bhattacharyya.prob | Bhattacharyya Distance, Coefficient and Probability

## -- C --

cell.Classify | immunoClust EMt-iteration on Cell-events given initial Model Parameters
cell.classifyAll | Clustering of Cell-events in the immunoClust-pipeline
cell.ClustData | Model Based Clustering of Data for a pre-defined Number of Clusters
cell.EM | immunoClust EMt-iteration on Cell-events given initial Model Parameters
cell.EMstep | immunoClust EMt-iteration on Cell-events given initial Model Parameters
cell.EMt | immunoClust EMt-iteration on Cell-events given initial Model Parameters
cell.Estep | immunoClust EMt-iteration on Cell-events given initial Model Parameters
cell.Estimation | immunoClust EMt-iteration on Cell-events given initial Model Parameters
cell.FitModel | immunoClust EMt-iteration on Cell-events given initial Model Parameters
cell.hclust | Hierarchical Model Based Clustering of Cell-events in the immunoClust-pipeline
cell.InitialModel | Clustering of Cell-events in the immunoClust-pipeline
cell.MajorIterationLoop | Clustering of Cell-events in the immunoClust-pipeline
cell.MajorIterationTrans | Clustering of Cell-events in the immunoClust-pipeline
cell.ME | immunoClust EM-iteration on Cell-events given initial Cluster Membership Assignment
cell.MEstep | immunoClust EM-iteration on Cell-events given initial Cluster Membership Assignment
cell.Mstep | immunoClust EM-iteration on Cell-events given initial Cluster Membership Assignment
cell.process | Clustering of Cell-events in the immunoClust-pipeline
cell.SubClustering | immunoClust Model Refinement Step in iterative Cell-events Clustering
cell.TestSubCluster | immunoClust Model Refinement Step in iterative Cell-events Clustering
cells | Acessors and Methods for immunoClust Objects
cells-method | Acessors and Methods for immunoClust Objects
classified | Acessors and Methods for immunoMeta Objects
classified-method | Acessors and Methods for immunoMeta Objects
classified.immunoMeta | Acessors and Methods for immunoMeta Objects
clusterCoeff | Generic function definitions in immunoClust
clusterCoeff-method | Acessors and Methods for immunoMeta Objects
clusterDist | Generic function definitions in immunoClust
clusterDist-method | Acessors and Methods for immunoMeta Objects
clusterProb | Generic function definitions in immunoClust
clusterProb-method | Acessors and Methods for immunoMeta Objects
clusters | Acessors and Methods for immunoMeta Objects
clusters-method | Acessors and Methods for immunoMeta Objects
clusters.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- D --

dat.exp | immunoClust Meta-clustering Sample
dat.fcs | immunoClust Cell-clustering Sample
dat.meta | immunoClust Meta-clustering Results Sample
datSplom | Scatterplot Matrix of immunoClust Clustering Results
desc | Acessors and Methods for immunoMeta Objects
desc-method | Acessors and Methods for immunoMeta Objects
desc.immunoMeta | Acessors and Methods for immunoMeta Objects
desc<- | Acessors and Methods for immunoMeta Objects
desc<--method | Acessors and Methods for immunoMeta Objects
desc<-.immunoMeta | Acessors and Methods for immunoMeta Objects
descFull | Acessors and Methods for immunoMeta Objects
descFull-method | Acessors and Methods for immunoMeta Objects
descFull.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- E --

events | Acessors and Methods for immunoMeta Objects
events-method | Acessors and Methods for immunoClust Objects
events-method | Acessors and Methods for immunoMeta Objects
events.immunoClust | Acessors and Methods for immunoClust Objects
events.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- F --

finalize | Acessors and Methods for immunoMeta Objects
finalize-method | Acessors and Methods for immunoMeta Objects
finalize.immunoMeta | Acessors and Methods for immunoMeta Objects
findLevel | Acessors and Methods for immunoMeta Objects
findLevel-method | Acessors and Methods for immunoMeta Objects
findLevel.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- I --

immunoClust | immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
immunoClust-class | immunoClust-Object
immunoClust.object | immunoClust-Object
immunoClust.package | immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
immunoMeta | 'immunoMeta': a class for storing meta-clustering results
immunoMeta-class | 'immunoMeta': a class for storing meta-clustering results
immunoMeta-object | 'immunoMeta': a class for storing meta-clustering results
immunoMeta.class | 'immunoMeta': a class for storing meta-clustering results
immunoMeta.object | 'immunoMeta': a class for storing meta-clustering results

## -- L --

label | Generic function definitions in immunoClust
label-method | Acessors and Methods for immunoClust Objects
label-method | Acessors and Methods for immunoMeta Objects
label.immunoClust | Acessors and Methods for immunoClust Objects
label.immunoMeta | Acessors and Methods for immunoMeta Objects
level | Acessors and Methods for immunoMeta Objects
level-method | Acessors and Methods for immunoMeta Objects
level.immunoMeta | Acessors and Methods for immunoMeta Objects
level<- | Acessors and Methods for immunoMeta Objects
level<-.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- M --

meta.Clustering | Clustering of Cell-clusters in the immunoClust-pipeline
meta.export | immunoClust Meta-clustering Results Export
meta.exprs | Collecting Data of an immunoClust vector
meta.freqTable | immunoClust Meta-clustering Results Export
meta.hclust | Hierarchical Meta-clustering of Cell-clusters in the immunoClust-pipeline
meta.majorEvents | immunoClust Meta-clustering Results Export
meta.ME | immunoClust EM(t)-iteration on Cell-clusters
meta.Normalize | immunoClust normalization step with the meta.clustering process
meta.numClusters | immunoClust Meta-clustering Results Export
meta.numEvents | immunoClust Meta-clustering Results Export
meta.parMFI | immunoClust Meta-clustering Results Export
meta.process | Meta-clustering of Cell-clusters in the immunoClust-pipeline
meta.RegNorm | immunoClust normalization procedure
meta.relEvents | immunoClust Meta-clustering Results Export
meta.relEvents2 | immunoClust Meta-clustering Results Export
meta.relEvents3 | immunoClust Meta-clustering Results Export
meta.relParent | immunoClust Meta-clustering Results Export
meta.SON.clustering | meta clustering process with internal SON normalisation
meta.SON.combineClustering | Transfer the annotation of an immunoMeta-object to an immunoClust-object.
meta.SubClustering | immunoClust Model Refinement Step in iterative Meta-clustering
meta.TestSubCluster | immunoClust Model Refinement Step in iterative Meta-clustering
move<- | Acessors and Methods for immunoMeta Objects
move<-.immunoMeta | Acessors and Methods for immunoMeta Objects
mu | Generic function definitions in immunoClust
mu-method | Acessors and Methods for immunoClust Objects
mu-method | Acessors and Methods for immunoMeta Objects
mu.immunoClust | Acessors and Methods for immunoClust Objects
mu.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- N --

ncls | Generic function definitions in immunoClust
ncls-method | Acessors and Methods for immunoClust Objects
ncls-method | Acessors and Methods for immunoMeta Objects
ncls.immunoClust | Acessors and Methods for immunoClust Objects
ncls.immunoMeta | Acessors and Methods for immunoMeta Objects
nobs | Generic function definitions in immunoClust
nobs-method | Acessors and Methods for immunoClust Objects
nobs-method | Acessors and Methods for immunoMeta Objects
nobs.immunoClust | Acessors and Methods for immunoClust Objects
nobs.immunoMeta | Acessors and Methods for immunoMeta Objects
npar | Generic function definitions in immunoClust
npar-method | Acessors and Methods for immunoClust Objects
npar-method | Acessors and Methods for immunoMeta Objects
npar.immunoClust | Acessors and Methods for immunoClust Objects
npar.immunoMeta | Acessors and Methods for immunoMeta Objects
nsam | Generic function definitions in immunoClust
nsam-method | Acessors and Methods for immunoMeta Objects
nsam.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- P --

parameters | Generic function definitions in immunoClust
parameters-method | Acessors and Methods for immunoClust Objects
parameters-method | Acessors and Methods for immunoMeta Objects
parameters.immunoClust | Acessors and Methods for immunoClust Objects
parameters.immunoMeta | Acessors and Methods for immunoMeta Objects
parameters<- | Generic function definitions in immunoClust
parameters<--method | Acessors and Methods for immunoClust Objects
parameters<--method | Acessors and Methods for immunoMeta Objects
parameters<-.immunoClust | Acessors and Methods for immunoClust Objects
parameters<-.immunoMeta | Acessors and Methods for immunoMeta Objects
parent<- | Acessors and Methods for immunoMeta Objects
parent<-.immunoMeta | Acessors and Methods for immunoMeta Objects
parent<-.immunoMeta-method | Acessors and Methods for immunoMeta Objects
plot-method | Scatterplot of immunoClust Clustering Results
plot-method | Scatterplot of immunoMeta Structured Clustering Results
plot.immunoClust | Scatterplot of immunoClust Clustering Results
plot.immunoMeta | Scatterplot of immunoMeta Structured Clustering Results
prop | Acessors and Methods for immunoMeta Objects
prop-method | Acessors and Methods for immunoMeta Objects
prop.immunoMeta | Acessors and Methods for immunoMeta Objects
prop<- | Acessors and Methods for immunoMeta Objects
prop<--method | Acessors and Methods for immunoMeta Objects
prop<-.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- R --

remove<- | Acessors and Methods for immunoMeta Objects
remove<-.immunoMeta | Acessors and Methods for immunoMeta Objects
removed.above | Brief Information of removed Cell-events by immunoClust Cell-event Clustering
removed.below | Brief Information of removed Cell-events by immunoClust Cell-event Clustering

## -- S --

sam_clsEvents | Generic function definitions in immunoClust
sam_clsEvents-method | Acessors and Methods for immunoMeta Objects
sam_clsEvents.immunoMeta | Acessors and Methods for immunoMeta Objects
sam_clsMu | Generic function definitions in immunoClust
sam_clsMu-method | Acessors and Methods for immunoMeta Objects
sam_clsMu.immunoMeta | Acessors and Methods for immunoMeta Objects
sam_clsSigma | Generic function definitions in immunoClust
sam_clsSigma-method | Acessors and Methods for immunoMeta Objects
sam_clsSigma.immunoMeta | Acessors and Methods for immunoMeta Objects
sam_clsWeights | Generic function definitions in immunoClust
sam_clsWeights-method | Acessors and Methods for immunoMeta Objects
sam_clsWeights.immunoMeta | Acessors and Methods for immunoMeta Objects
sam_ncls | Generic function definitions in immunoClust
sam_ncls-method | Acessors and Methods for immunoMeta Objects
sam_ncls.immunoMeta | Acessors and Methods for immunoMeta Objects
show | immunoClust-Object
show-method | immunoClust-Object
show-method | 'immunoMeta': a class for storing meta-clustering results
show.immunoClust | immunoClust-Object
show.immunoMeta | 'immunoMeta': a class for storing meta-clustering results
sigma | Generic function definitions in immunoClust
sigma-method | Acessors and Methods for immunoClust Objects
sigma-method | Acessors and Methods for immunoMeta Objects
sigma.immunoClust | Acessors and Methods for immunoClust Objects
sigma.immunoMeta | Acessors and Methods for immunoMeta Objects
splom | Scatterplot Matrix of immunoClust Clustering Results
splom-method | Scatterplot Matrix of immunoClust Clustering Results
splom.immunoClust | Scatterplot Matrix of immunoClust Clustering Results
subset | Generic function definitions in immunoClust
subset-method | Acessors and Methods for immunoClust Objects
subset-method | Acessors and Methods for immunoMeta Objects
subset.immunoClust | Acessors and Methods for immunoClust Objects
subset.immunoMeta | Acessors and Methods for immunoMeta Objects
summary | immunoClust-Object
summary-method | immunoClust-Object
summary-method | 'immunoMeta': a class for storing meta-clustering results
summary.immunoClust | immunoClust-Object
summary.immunoMeta | 'immunoMeta': a class for storing meta-clustering results

## -- T --

trans.ApplyToData | immunoClust asinh-Transformation
trans.FitToData | immunoClust asinh-Transformation Optimization
transfer<- | Acessors and Methods for immunoMeta Objects
transfer<--method | Acessors and Methods for immunoMeta Objects
transfer<-.immunoMeta | Acessors and Methods for immunoMeta Objects
transformParams | Generic function definitions in immunoClust
transformParams-method | Acessors and Methods for immunoClust Objects
transformParams-method | Acessors and Methods for immunoMeta Objects
transformParams.immunoClust | Acessors and Methods for immunoClust Objects
transformParams.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- U --

unclassified | Acessors and Methods for immunoMeta Objects
unclassified-method | Acessors and Methods for immunoMeta Objects
unclassified.immunoMeta | Acessors and Methods for immunoMeta Objects

## -- W --

weights | Generic function definitions in immunoClust
weights-method | Acessors and Methods for immunoClust Objects
weights-method | Acessors and Methods for immunoMeta Objects
weights.immunoClust | Acessors and Methods for immunoClust Objects
weights.immunoMeta | Acessors and Methods for immunoMeta Objects