cluster_embedding: Cluster the resulting embedding

In kieranrcampbell/embeddr: Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Description

Cluster the embedded representation using either kmeans or mixture models from the mclust package

Usage

cluster_embedding(sce, method = c("mm", "kmeans"), k = NULL)

Arguments

sce	The SCESet object
method	Either 'kmeans' or 'mm' to use mclust
k	The number of clusters to find in the data

Value

The dataframe M with a new numeric variable 'cluster' containing the assigned cluster

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)
sce <- cluster_embedding(sce)

kieranrcampbell/embeddr documentation built on May 20, 2019, 9:24 a.m.