sc_clustering.HAC: Perform Single Cell data clustering using Hierarchical...

In pengminshi/MRtree: Multi-resolution Reconciled Tree

Perform Single Cell data clustering using Hierarchical Agglomerative clustering (HAC)

Description

Perform Single Cell data clustering using Hierarchical Agglomerative clustering (HAC)

Usage

sc_clustering.HAC(
  exprs,
  n.pcs = 10,
  labels = NULL,
  method = "complete",
  type = c("count", "log"),
  scale.factor = 10000,
  verbose = FALSE
)

Arguments

exprs	n.genes-by-n.cells expression matrix
n.pcs	integer, number of principal components to use for calculating similarity and performn HAC
labels	vector of string/factor, if provided, HAC is performed starting from clusters
method	string, similarity method, one of 'ward.D', 'ward.D2', 'single', 'complete', 'average' (= UPGMA), 'mcquitty' (= WPGMA), 'median' (= WPGMC) or 'centroid' (= UPGMC).
type	string, type of the expression matrix, choices are 'count' and 'log', and default by 'counts
scale.factor	scalar sets the scale factor for cell-level normalization
verbose	boolean, whether to print messages

Value

an hclust object containing the clustering results

pengminshi/MRtree documentation built on March 6, 2023, 4:20 p.m.