choose_cluster_scExp {ChromSCape} | R Documentation

## Choose a number of clusters

### Description

This functions takes as input a SingleCellExperiment object with consclust and a number of cluster to select. It outputs a SingleCellExperiment object with each cell assigned to a correlation cluster in colData. Also calculates a hierarchical clustering of the consensus associations calculated by ConsensusClusterPlus.

### Usage

    choose_cluster_scExp(
      scExp,
      nclust = 3,
      consensus = FALSE,
      hc_linkage = "ward.D"
    )

### Arguments

`scExp` | A SingleCellExperiment object containing consclust in metadata.
`nclust` | Number of cluster to pick (3)
`consensus` | Use consensus clustering results instead of simple hierarchical clustering ? (FALSE)
`hc_linkage` | A linkage method for hierarchical clustering. See cor. ('ward.D')

### Value

Returns a SingleCellExperiment object with each cell assigned to a correlation cluster in colData.

### Examples

    data("scExp")
    scExp_cf = correlation_and_hierarchical_clust_scExp(scExp)
    scExp_cf = choose_cluster_scExp(scExp_cf,nclust=3,consensus=FALSE)
    table(scExp_cf$cell_cluster)

    scExp_cf = consensus_clustering_scExp(scExp)
    scExp_cf_consensus = choose_cluster_scExp(scExp_cf,nclust=3,consensus=TRUE)
    table(scExp_cf_consensus$cell_cluster)

[Package ChromSCape version 1.2.62 Index]