Performs SCTransform

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

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')
#> Error in is(object = object, class2 = "IBRAP"): object 'object' not found