flowSOM.MC {MetaCyto} | R Documentation

## Cluster cytometry data using FlowSOM

### Description

A function that cluster cytometry data using FlowSOM.

### Usage

    flowSOM.MC(fcsFrame, excludeClusterParameters, xdim = 10, ydim = 10,
      k = 40, seed = NULL)

### Arguments

`fcsFrame` | A flow frame.
`excludeClusterParameters` | A vector specifying the name of markers not to be used for clustering.
`xdim` | An integer, defines the width of SOM
`ydim` | An integer, defines the height of SOM
`k` | An integer, defines the number of clusters to be identified by flowSOM.
`seed` | Set seed for reproducible results.

### 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 flowSOM.MC
    cluster_list=flowSOM.MC(fcsFrame=fcs,
                            excludeClusterParameters=c("Time","Cell_length"))

[Package MetaCyto version 1.4.0 Index]