flowHC: Cluster cytometry data using hierarchical clustering

In MetaCyto: MetaCyto: A package for meta-analysis of cytometry data

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"))

MetaCyto documentation built on Nov. 8, 2020, 7:50 p.m.