citrus.selectClusters: Select clusters for further analysis

In nolanlab/citrus: Citrus: Identification of stratifying subpopulations in Flow Cytometry Data.

Select clusters for further analysis

Description

Selects clusters from a set of clusters identified by a clustering method investigate for stratifying signal.

Usage

citrus.selectClusters(citrus.clustering, method = "minimumClusterSize", ...)

Arguments

citrus.clustering	A citrus.clustering object.
method	Method for determining which clusters from a clustering should be analyzed for stratifying signal.
...	Other parameters passed to specific cluster selection methods.

Value

A vector of cluster IDs.

Author(s)

Robert Bruggner

See Also

citrus.selectClusters.minimumClusterSize.

Examples

# Where the data lives
dataDirectory = file.path(system.file(package = "citrus"),"extdata","example1")

# Create list of files to be analyzed
fileList = data.frame("unstim"=list.files(dataDirectory,pattern=".fcs"))

# Read the data
citrus.combinedFCSSet = citrus.readFCSSet(dataDirectory,fileList)

# List of columns to be used for clustering
clusteringColumns = c("Red","Blue")

# Cluster data
citrus.clustering = citrus.cluster(citrus.combinedFCSSet,clusteringColumns)

# Select clusters that contain at least 1% of clustered events.
largeEnoughClusters = citrus.selectClusters(citrus.clustering,minimumClusterSizePercent=0.01)

nolanlab/citrus documentation built on April 19, 2024, 6:49 p.m.