Performs PCA reduction — perform.pca • IBRAP

Performs PCA reduction on defined method-assays. Data should be HVG subset, normalised and scaled (in the norm.scaled assay)

perform.pca(
  object,
  assay,
  slot = "norm.scaled",
  n.pcs = 50,
  reduction.save = "PCA",
  print.variance = FALSE,
  verbose = FALSE,
  seed = 1234,
  ...
)

Arguments

object: IBRAP S4 class object
assay: Character. String containing indicating which assay to use
slot: Character. String indicating which slot within the assay should be sourced
n.pcs: Numerical. How many principal components should be produced. Default = 50
reduction.save: Character. What should this reduction be saved as in computation_reduction. Default = 'pca'
print.variance: Logical. Should the plot be printed to the console
...: Arguments to be passed to PCAtools::pca

Value

PCA reductions contained within the computational_reduction list in the defined assays

Examples


object <- perform.pca(object = object, 
                      assay = c('SCT', 'SCRAN', 'SCANPY'), 
                      n.pcs = 50, 
                      reduction.save = 'pca')
#> Error in is(object = object, class2 = "IBRAP"): object 'object' not found