Matching and meta-clustering in flow cytometry


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Documentation for package ‘flowMatch’ version 1.34.0

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flowMatch-package Matching cell populations and building meta-clusters and templates from a collection of FC samples.
Cluster Cluster: A class representing a cell population in FC
Cluster-class Cluster: A class representing a cell population in FC
ClusteredSample ClusteredSample: A class representing a clustered FC Sample
ClusteredSample-class ClusteredSample: A class representing a clustered FC Sample
ClusterMatch ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
ClusterMatch-class ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
create.template Creating a template of a collection of FC samples
dist.cluster Dissimilarity between a pair of clusters
dist.matrix Dissimilarity matrix between each pair of clusters/meta-clusters across a pair of samples/templates
dist.sample Dissimilarity between a pair of clustered FC samples
dist.template Dissimilarity between a pair of FC templates
flowMatch Matching cell populations and building meta-clusters and templates from a collection of FC samples.
get.center Cluster: A class representing a cell population in FC
get.center-method Cluster: A class representing a cell population in FC
get.center-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
get.cluster.id Cluster: A class representing a cell population in FC
get.cluster.id-method Cluster: A class representing a cell population in FC
get.clusters ClusteredSample: A class representing a clustered FC Sample
get.clusters-method ClusteredSample: A class representing a clustered FC Sample
get.clusters-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
get.cov Cluster: A class representing a cell population in FC
get.cov-method Cluster: A class representing a cell population in FC
get.cov-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
get.dimension ClusteredSample: A class representing a clustered FC Sample
get.dimension-method ClusteredSample: A class representing a clustered FC Sample
get.dimension-method Template: An S4 class representing a template of a group of FC Samples.
get.labels ClusteredSample: A class representing a clustered FC Sample
get.labels-method ClusteredSample: A class representing a clustered FC Sample
get.match12 ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
get.match12-method ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
get.match21 ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
get.match21-method ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
get.matching.cost ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
get.matching.cost-method ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
get.metaClusters Template: An S4 class representing a template of a group of FC Samples.
get.metaClusters-method Template: An S4 class representing a template of a group of FC Samples.
get.num.clusters ClusteredSample: A class representing a clustered FC Sample
get.num.clusters-method ClusteredSample: A class representing a clustered FC Sample
get.num.clusters-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
get.num.metaclusters Template: An S4 class representing a template of a group of FC Samples.
get.num.metaclusters-method Template: An S4 class representing a template of a group of FC Samples.
get.sample.id Cluster: A class representing a cell population in FC
get.sample.id-method Cluster: A class representing a cell population in FC
get.sample.id-method ClusteredSample: A class representing a clustered FC Sample
get.size Cluster: A class representing a cell population in FC
get.size-method Cluster: A class representing a cell population in FC
get.size-method ClusteredSample: A class representing a clustered FC Sample
get.size-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
get.size-method Template: An S4 class representing a template of a group of FC Samples.
get.template.id Template: An S4 class representing a template of a group of FC Samples.
get.template.id-method Template: An S4 class representing a template of a group of FC Samples.
get.tree Template: An S4 class representing a template of a group of FC Samples.
get.tree-method Template: An S4 class representing a template of a group of FC Samples.
get.unmatch.penalty ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
get.unmatch.penalty-method ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
mahalanobis.dist Mahanalobis Distance
match.clusters Matching of clusters/meta-clusters across FC samples/templates
match.clusters.dist Matching of clusters/meta-clusters across FC samples/templates
MetaCluster MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
MetaCluster-class MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
plot-method ClusteredSample: A class representing a clustered FC Sample
plot-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
plot-method Template: An S4 class representing a template of a group of FC Samples.
sample.id<- Cluster: A class representing a cell population in FC
sample.id<--method Cluster: A class representing a cell population in FC
show-method Cluster: A class representing a cell population in FC
show-method ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
show-method ClusteredSample: A class representing a clustered FC Sample
show-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
show-method Template: An S4 class representing a template of a group of FC Samples.
summary-method Cluster: A class representing a cell population in FC
summary-method ClusterMatch: A class representing matching of cluster/meta-clusters across a pair of FC samples/templates
summary-method ClusteredSample: A class representing a clustered FC Sample
summary-method MetaCluster: An S4 class representing a meta-cluster (collection of biologically similar clusters).
summary-method Template: An S4 class representing a template of a group of FC Samples.
symmetric.KL Symmetrized Kullback-Leibler divergence
Template Template: An S4 class representing a template of a group of FC Samples.
Template-class Template: An S4 class representing a template of a group of FC Samples.
template.tree Plot the hierarchy of samples established while creating a template-tree
template.tree-method Plot the hierarchy of samples established while creating a template-tree