Runs SCTransform with mode-aware defaults.
In transcript mode (long-read), normalises the "isoform"
assay by default, so that transcript-level abundances are variance-stabilised
before dimensionality reduction. In junction mode (short-read),
normalises the active default assay (typically "RNA").
Usage
# S3 method for class 'MatisseObject'
SCTransform(object, assay = NULL, vars_to_regress = NULL, verbose = TRUE, ...)Arguments
- object
A
MatisseObject.- assay
Character. Assay to normalise. Default:
"isoform"in transcript mode; the active default assay in junction mode.- vars_to_regress
Character vector. Covariates to regress out (e.g.
"percent.mt"). Default:NULL.- verbose
Logical. Print progress messages. Default:
TRUE.- ...
Additional arguments forwarded to
SCTransform.
Details
Override the target assay with the assay argument. PCA is
not run automatically — call RunPCA.MatisseObject
after normalisation:
obj <- SCTransform(obj) # normalise
obj <- RunPCA(obj, assay = "SCT", npcs = 50) # reduce
obj <- RunUMAP(obj, dims = 1:50) # embed