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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.
calcARI(object, clusters.compare, verbose = TRUE)
Adjusted Rand index value.
liger
object. Should run quantileAlignSNF before calling.
Clustering with which to compare (named vector).
Print messages (TRUE by default)
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)
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