Calculate adjusted Rand index
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)
object |
|
clusters.compare |
Clustering with which to compare (named vector). |
verbose |
Print messages (TRUE by default) |
Adjusted Rand index value.
## Not run:
# ligerex (liger object), factorization complete
ligerex <- quantile_norm(ligerex)
# toy clusters
cluster1 <- sample(c('type1', 'type2', 'type3'), ncol(ligerex@raw.data[[1]]), replace = TRUE)
names(cluster1) <- colnames(ligerex@raw.data[[1]])
cluster2 <- sample(c('type4', 'type5', 'type6'), ncol(ligerex@raw.data[[2]]), replace = TRUE)
names(cluster2) <- colnames(ligerex@raw.data[[2]])
# get ARI for first clustering
ari1 <- calcARI(ligerex, cluster1)
# get ARI for second clustering
ari2 <- calcARI(ligerex, cluster2)
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