immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

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Documentation for package ‘immunoClust’ version 1.36.0

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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