calcARI: Calculate adjusted Rand index

In rliger: Linked Inference of Genomic Experimental Relationships

Calculate adjusted Rand index

Description

Computes adjusted Rand index for liger clustering and external clustering. The Rand index ranges from 0 to 1, with 0 indicating no agreement between clusterings and 1 indicating perfect agreement.

Usage

calcARI(object, clusters.compare, verbose = TRUE)

Arguments

object	liger object. Should run quantileAlignSNF before calling.
clusters.compare	Clustering with which to compare (named vector).
verbose	Print messages (TRUE by default)

Value

Adjusted Rand index value.

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
# Specification for minimal example run time, not converging
ligerex <- optimizeALS(ligerex, k = 5, max.iters = 1)
ligerex <- quantile_norm(ligerex)
agreement <- calcARI(ligerex, ligerex@clusters)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.