correlation_and_hierarchical_clust_scExp {ChromSCape} | R Documentation

## Correlation and hierarchical clustering

### Description

Calculates cell to cell correlation matrix based on the PCA feature space and runs hierarchical clustering taking 1 - correlation scores as distance.

### Usage

    correlation_and_hierarchical_clust_scExp(scExp, hc_linkage = "ward.D")

### Arguments

`scExp` | A SingleCellExperiment object, containing 'PCA' in reducedDims.
`hc_linkage` | A linkage method for hierarchical clustering. See cor. ('ward.D')

### Details

This functions takes as input a SingleCellExperiment object that must have PCA calculated and outputs a SingleCellExperiment object with correlation matrix and hierarchical clustering.

### Value

Return a SingleCellExperiment object with correlation matrix & hiearchical clustering.

### Examples

    data("scExp")
    scExp_cf = correlation_and_hierarchical_clust_scExp(scExp)

[Package ChromSCape version 1.2.62 Index]