correlation_and_hierarchical_clust_scExp {ChromSCape} | R Documentation |
Calculates cell to cell correlation matrix based on the PCA feature space and runs hierarchical clustering taking 1 - correlation scores as distance.
correlation_and_hierarchical_clust_scExp( scExp, correlation = "pearson", hc_linkage = "ward.D" )
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') |
This functions takes as input a SingleCellExperiment object that must have PCA calculated and outputs a SingleCellExperiment object with correlation matrix and hierarchical clustering.
Return a SingleCellExperiment object with correlation matrix & hiearchical clustering.
data("scExp") scExp_cf = correlation_and_hierarchical_clust_scExp(scExp)