metaclusterDiscovrExperiment: Perform metaclustering for a DISCOV-R experiment

In BenaroyaResearch/briDiscovr: Distribution analysis across clusters of a parent population overlaid with a rare subpopulation

Perform metaclustering for a DISCOV-R experiment

Description

Perform metaclustering for a DISCOV-R experiment

Usage

metaclusterDiscovrExperiment(
  experiment,
  dropSamples = NA,
  dropMarkers = NA,
  pctInClusterThreshold = 1,
  nMetaclusters = 12,
  linkage = "ward.D2",
  distance = "euclidean",
  verbose = TRUE
)

Arguments

experiment	A discovrExperiment created using setupDiscovrExperiment and clustered using clusterDiscovrExperiment
dropSamples	A string or vector of strings indicating names of samples to exclude from further analysis. Note that the convenience function getSampleNames can be used to view a list of all sample names. (default: NA)
dropMarkers	A string or vector of strings indicating names of markers to exclude from analysis. Note that printing the experiment object will display a list of all markers. By default all clustering markers will be included. (default: NA)
pctInClusterThreshold	A numeric indicating a percentage. Cluster with event occupancy below this threshold will be considered 'low-abundance' and will be dropped from further analysis (default: 1)
nMetaclusters	A numeric indicating the number of metaclusters to generate (default: 12)
linkage	A string indicating the cluster linkage method to use when metaclustering. See hclust for more details. (default: "ward.D2")
distance	A string indicating the distance metric to use when metaclustering. (default: "euclidean")
verbose	A boolean specifying whether to display processing messages (default: TRUE)

Value

An S3 object of class discovrExperiment

Author(s)

Mario G Rosasco, Virginia Muir

See Also

setupDiscovrExperiment clusterDiscovrExperiment

BenaroyaResearch/briDiscovr documentation built on March 15, 2024, 12:31 a.m.