Normalize Expression for GiottoDB with dbMatrix support

For GiottoDB objects with dbMatrix expression, scaling (centering) is handled implicitly during PCA via db_svd. If scale_feats or scale_cells are TRUE, a warning is emitted and both are silently forced to FALSE. No "scaled" expression slot is created.

Usage

normalizeGiotto(gobject, ...)

# S3 method for class 'GiottoDB'
normalizeGiotto(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = "raw",
  norm_methods = c("standard", "pearson_resid", "osmFISH", "quantile"),
  library_size_norm = TRUE,
  scalefactor = 6000,
  log_norm = TRUE,
  log_offset = 1,
  logbase = 2,
  scale_feats = TRUE,
  scale_genes = lifecycle::deprecated(),
  scale_cells = TRUE,
  scale_order = c("first_feats", "first_cells"),
  theta = 100,
  name = "scaled",
  update_slot = lifecycle::deprecated(),
  verbose = TRUE,
  ...
)

# S3 method for class 'giotto'
normalizeGiotto(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = "raw",
  norm_methods = c("standard", "pearson_resid", "osmFISH", "quantile"),
  library_size_norm = TRUE,
  scalefactor = 6000,
  log_norm = TRUE,
  log_offset = 1,
  logbase = 2,
  scale_feats = TRUE,
  scale_genes = lifecycle::deprecated(),
  scale_cells = TRUE,
  scale_order = c("first_feats", "first_cells"),
  theta = 100,
  name = "scaled",
  update_slot = lifecycle::deprecated(),
  verbose = TRUE,
  ...
)

Arguments

gobject

A giotto or GiottoDB object

...

Additional arguments passed to Giotto::normalizeGiotto

scale_feats

Not supported for GiottoDB. Forced to FALSE with a warning. Centering is performed inside runPCA via db_svd.

scale_cells

Not supported for GiottoDB. Forced to FALSE with a warning. Centering is performed inside runPCA via db_svd.

Details

S3 generic that dispatches to Giotto::normalizeGiotto with optimizations for dbMatrix::dbMatrix-backed expression data.