flowSOM.MC {MetaCyto}R Documentation

Cluster cytometry data using FlowSOM

Description

A function that cluster cytometry data using FlowSOM.

Usage

flowSOM.MC(fcsFrame, excludeClusterParameters, grid = 10, k = 40)

Arguments

fcsFrame

A flow frame.

excludeClusterParameters

A vector specifying the name of markers not to be used for clustering.

grid

An integer, defines the width and height of SOM

k

An integer, defines the number of clusters to be identified by flowSOM.

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 1.2.1 Index]