perform.sct: Performs SCTransform

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

Performs SCTransform

Description

Performs SCTransform normalisation, hvg selection, scaling and variance stabilisation and regression.

Usage

perform.sct(
  object,
  assay = "RAW",
  slot = "counts",
  new.assay.suffix = "",
  verbose = FALSE,
  seed = 1234,
  ...
)

Arguments

object	IBRAP S4 class object
assay	A character string containing indicating which assay to use
slot	String indicating which slot within the assay should be sourced
new.assay.suffix	Character. What should be added as a suffix for SCT
verbose	Logical Should function messages be printed?
seed	Numerical What seed should be set. Default = 1234
do.scale	Whether to scale residuals to have unit variance; default is FALSE
do.center	Whether to center residuals to have mean zero; default is TRUE
vars.to.regress	Character. Which data from 'object@sample_metadata' should be regressed from the dataset.
n.genes	Numerical value of how many highly variable genes should be retained. Default = 1500
min_cells	Numerical value of minimum cells required for a gene to not be filtered. Default = 3

Value

Produces a new 'methods' assay containing normalised, scaled and HVGs.

Examples

object <- perform.sct(object = object, 
                      assay = 'RAW', 
                      slot = 'counts')

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