flowHC {MetaCyto} | R Documentation

## Cluster cytometry data using hierarchical clustering

### Description

A function that cluster cytometry data using hierarchical clustering.

### Usage

    flowHC(fcsFrame, excludeClusterParameters, minimumClusterSizePercent = 0.05)

### Arguments

`fcsFrame` | A flow frame.
`excludeClusterParameters` | A vector specifying the name of markers not to be used for clustering.
`minimumClusterSizePercent` | A number between 0 and 1, used to specify the minimum size of a cluster relative to all events.

### Value

A list of clusters. Each cluster contains the ID of all cells that belong to the cluster.

### Examples

    # Find fcs files
    files=system.file("extdata","SDY420/ResultFiles/CyTOF_result",
                     package="MetaCyto")
    files=list.files(files,pattern="fcs$",full.names=TRUE)
    # Preprocess
    fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8)
    # cluster using flowHC
    cluster_list=flowHC(fcsFrame=fcs,
                        excludeClusterParameters=c("Time","Cell_length"))

[Package MetaCyto version 1.2.1 Index]