SCTransform normalisation for MatisseObjects

Runs SCTransform with mode-aware defaults. In event mode, normalises the "transcript" assay. In junction mode, normalises the active default assay (usually "RNA"). Override with the assay argument.

Usage

# S3 method for class 'MatisseObject'
SCTransform(
  object,
  assay = NULL,
  n_pca_dims = 50L,
  vars_to_regress = NULL,
  verbose = TRUE,
  ...
)

Arguments

object

A MatisseObject.

assay

Character. Assay to normalise. Default: "transcript" in event mode; the active default assay in junction mode.

n_pca_dims

Integer. PCA dimensions to compute. Default: 50. Set to 0L to skip PCA.

vars_to_regress

Character vector. Variables to regress out. Default: NULL.

verbose

Logical. Default: TRUE.

...

Additional arguments forwarded to SCTransform.

Value

The updated MatisseObject.

Details

After normalisation, RunPCA is run automatically on the resulting "SCT" assay. To skip PCA set n_pca_dims = 0L.