distributionDistance: Computes the distribution distance

In cn.farms: cn.FARMS - factor analysis for copy number estimation

Description

Be aware that this function is implemented quite slow.

Usage

distributionDistance(intensityData, method = c("JSDiv", "KLDiv", "KLInf"),
  useSubset = T, subsetFraction = 0.25, useQuantileReference = FALSE)

Arguments

intensityData	A matrix or an AffyBatch object.
method	The method you want to use.
useSubset	Logical. States if only a subset should be used.
subsetFraction	The fraction of the subset.
useQuantileReference	Logical for a quantile reference.

Value

Computes the distribution distance

Author(s)

Djork-Arne Clevert [e-mail] and Andreas Mitterecker [e-mail]

Examples

load(system.file("exampleData/normData.RData", package = "cn.farms"))
x <- assayData(normData)$intensity[, 1:3]
y <- distributionDistance(x)
attr(y, "Labels") <- substr(sampleNames(normData), 1, 7)
plotDendrogram(y)

cn.farms documentation built on Nov. 8, 2020, 7:59 p.m.