scCluster: Single-cell Clustering

In VCCRI/CIDR: Clustering through Imputation and Dimensionality Reduction

Description

performs heirarchical clustering on CIDR principal coordinates.

Usage

## S4 method for signature 'scData'
scCluster(object, n = NULL, nCluster = NULL,
  nPC = NULL, cMethod = "ward.D2")

Arguments

object	an scData class object.
n	Calinski-Harabasz Index is used to decide which number between 2 and n is optimal as the number of clusters; if NULL (default), it is set to be nPC*2+2. User should not assign both n and nCluster.
nCluster	the number of clusters; if NULL (default), it is determined automatically. User should not assign both n and nCluster.
nPC	the number of PCs used in clustering; by default 4.
cMethod	hierarchical clustering method; by default "ward.D2".

Value

an updated scData class object with the following attributes updated

nCluster	the number of clusters.
nPC	the number of PCs used in clustering.
clusters	a vector assigning each cell to a cluster.
cMethod	hierarchical clustering method.

Examples

example(cidr)

VCCRI/CIDR documentation built on May 9, 2019, 9:41 p.m.