perform.pca: Performs PCA reduction

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Performs PCA reduction

Description

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

Usage

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')

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.