Run PCA and store in DimReduction

Uses generatePCs() under the hood. If HVGs are empty, selects HVGs via FindVariableFeatures(object, nfeatures) with default nfeatures = 2000. If HVGs are present, the PCA uses NFEATURES = length(HVGs(object)). This aligns the PCA feature count with the HVG selection while allowing an explicit override of nfeatures when empty.

RunPCA(object, nfeatures = 2000)

Arguments

object

A geneda object

nfeatures

Number of features to use when HVGs are empty. Default = 2000

Value

Updated geneda object with DimReduction filled