calcAlignmentPerCluster: Calculate alignment for each cluster

In rliger: Linked Inference of Genomic Experimental Relationships

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 quantile_norm 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

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 <- calcAlignmentPerCluster(ligerex)

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