correlation_and_hierarchical_clust_scExp: Correlation and hierarchical clustering

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

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,
  correlation = "pearson",
  hc_linkage = "ward.D"
)

Arguments

scExp	A SingleCellExperiment object, containing 'PCA' in reducedDims.
correlation	A correlation method to use. See hclust. ('pearson')
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)

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.