# Matching and meta-clustering in flow cytometry

## Documentation for package ‘flowMatch’ version 1.4.0

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

## Help Pages

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