sc3_calc_consens: Calculate consensus matrix.

In hemberg-lab/SC3: Single-Cell Consensus Clustering

Description

This function calculates consensus matrices based on the clustering solutions contained in the kmeans item of the sc3 slot of the metadata(object). It then creates and populates the consensus item of the sc3 slot with consensus matrices, their hierarchical clusterings in hclust objects, and Silhouette indeces of the clusters. It also removes the previously calculated kmeans clusterings from the sc3 slot, as they are not needed for further analysis.

Usage

sc3_calc_consens.SingleCellExperiment(object)

## S4 method for signature 'SingleCellExperiment'
sc3_calc_consens(object)

Arguments

object

an object of SingleCellExperiment class

Details

Additionally, it also adds new columns to the colData slot of the input object. The column names correspond to the consensus cell labels and have the following format: sc3_k_clusters, where k is the number of clusters.

Value

an object of SingleCellExperiment class

hemberg-lab/SC3 documentation built on Dec. 18, 2019, 10:02 p.m.