normalizeDiscovrExperiment: Normalize marker expression within a DISCOV-R experiment

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

Normalize marker expression within a DISCOV-R experiment

Description

Normalize marker expression within a DISCOV-R experiment

Usage

normalizeDiscovrExperiment(
  experiment,
  normalizationInfo = NULL,
  defaultNormalizationMethod = "zScore",
  seed = 12345,
  verbose = TRUE
)

Arguments

experiment	A discovrExperiment created using setupDiscovrExperiment() and clustered using clusterDiscovrExperiment()
normalizationInfo	(default: NULL) Optional object containing information on how to normalize. If left NULL, the experiment object will be checked for normalization info in experiment$markerInfo$normalizationMethod. If that is not present, or for any markers without a method specified, normalization will use the default method, currently "zScore". Acceptable non-NULL values include a data frame with columns columns "commonMarkerName" and "normalizationMethod", a named vector with elements specifying normalization method and names referring to each marker in experiment$mergedExpr, or a single character value specifying the normalization method to be applied to all markers. Options for normalization are "zScore", "none", and "warpSet". In addition, "warpSet" can include a maximum peak number specification as a number immediately following (e.g. "warpSet2") - see documentation of flowStats::warpSet for details. Any markers lacking a specification will be normalized using the default method (currently "zScore").
defaultNormalizationMethod	(default: "zScore") A character string, the normalization method to use for markers without another method specified. Options are the same as in normalizationInfo above.
seed	(default: 12345) Numeric, the random number seed for warpSet normalization, passed to normalizeWarpSetMergedExpr
verbose	(default: TRUE) A logical specifying whether to display processing messages

Value

An S3 object of class discovrExperiment, with additional elements named "mergedExprNormalizedScaled" and "clusterMeansNormalizedScaled". If the normalization methods were not taken from experiment$markerInfo$normalizationMethod, the normalization method for each marker will be stored there.

Author(s)

Matt Dufort

See Also

discovrExperiment

BenaroyaResearch/briDiscovr documentation built on July 16, 2025, 7:13 p.m.