immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

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Documentation for package ‘immunoClust’ version 1.20.0

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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

-- 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.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.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
classified Acessors and Methods for immunoMeta Objects
classified-method Acessors and Methods for immunoMeta Objects
classified.immunoMeta 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.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.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.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<--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
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
posterior Generic function definitions in immunoClust
posterior-method Acessors and Methods for immunoClust Objects
posterior-method Acessors and Methods for immunoMeta Objects
posterior.immunoClust Acessors and Methods for immunoClust Objects
posterior.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
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<-.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