rliger (version 1.0.0)

calcAlignmentPerCluster: Calculate alignment for each cluster

Description

Returns alignment for each cluster in analysiss (see documentation for calcAlignment).

Usage

calcAlignmentPerCluster(object, rand.seed = 1, k = NULL, by.dataset = FALSE)

Arguments

object

liger object. Should call quantileAlignSNF before calling.

rand.seed

Random seed for reproducibility (default 1).

k

Number of nearest neighbors in calculating alignment (see calcAlignment for default). Can pass in single value or vector with same length as number of clusters.

by.dataset

Return alignment calculated for each dataset in cluster (default FALSE).

Value

Vector of alignment statistics (with names of clusters).

Examples

# NOT RUN {
# ligerex (liger object), factorization complete
ligerex <- quantile_norm(ligerex)
# get alignment for each cluster
alignment_per_cluster <- calcAlignmentPerCluster(ligerex)
# }