citrus.getRelatedClusterIds: Get ancestors or decendants of a cluster

In junyzhou10/test: Citrus: Identification of stratifying subpopulations in Flow Cytometry Data.

Description

Get ancestors or decendants of a cluster for hierarchical clustering

Usage

citrus.getClusterDecendants(clusterId, mergeOrder)

citrus.getClusterAncestors(clusterId, mergeOrder)

Arguments

clusterId	ID of a cluster for which to retreive related clusters.
mergeOrder	mergeOrder result from hclust object.

Value

Vector of cluster ids that are decendants of clusterId argument.

Author(s)

Robert Bruggner

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)

# Get decendants
citrus.getClusterDecendants(15000,citrus.clustering$clustering$merge)

# Get ancestors
citrus.getClusterAncestors(15000,citrus.clustering$clustering$merge)

junyzhou10/test documentation built on Nov. 4, 2019, 3:27 p.m.