rliger (version 1.0.0)

calcPurity: Calculate purity

Description

Calculates purity for liger clustering and external clustering (true clusters/classes). Purity can sometimes be a more useful metric when the clustering to be tested contains more subgroups or clusters than the true clusters (or classes). Purity also ranges from 0 to 1, with a score of 1 representing a pure, or accurate, clustering.

Usage

calcPurity(object, classes.compare, verbose = TRUE)

Arguments

object

liger object. Should run quantileAlignSNF before calling.

classes.compare

Clustering with which to compare (named vector).

verbose

Print messages (TRUE by default)

Value

Purity value.

Examples

# NOT RUN {
# ligerex (liger object), factorization complete
ligerex <- quantile_norm(ligerex)
# toy clusters
cluster1 <- sample(c('type1', 'type2', 'type3'), ncol([e-mail][[1]]), replace = TRUE)
names(cluster1) <- colnames([e-mail][[1]])
cluster2 <- sample(c('type4', 'type5', 'type6'), ncol([e-mail][[2]]), replace = TRUE)
names(cluster2) <- colnames([e-mail][[2]])
# get ARI for first clustering
ari1 <- calcPurity(ligerex, cluster1)
# get ARI for second clustering
ari2 <- calcPurity(ligerex, cluster2)
# }