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Find marker features one-vs-all with GiottoDB support

Source: R/findMarkers_S3.R
findMarkers_one_vs_all.Rd

S3 wrapper for Giotto::findMarkers_one_vs_all(). For GiottoDB inputs, the specific expression matrix (spat_unit/feat_type/expression_values) is materialized from dbMatrix to dgCMatrix before delegating to the Giotto implementation. Only the requested matrix is converted; all other slots remain database-backed.

Usage

findMarkers_one_vs_all(gobject, ...)

# S3 method for class 'GiottoDB'
findMarkers_one_vs_all(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  ...
)

# S3 method for class 'giotto'
findMarkers_one_vs_all(gobject, ...)

Arguments

gobject

A giotto or GiottoDB object

...

Additional arguments passed to Giotto::findMarkers_one_vs_all

spat_unit

spatial unit (default: object default)

feat_type

feature type (default: object default)

expression_values

expression values to use

Value

data.table of marker results

Note

For methods that call subsetGiotto() internally (e.g. "gini", "mast"), this wrapper creates a minimal in-memory giotto marker object from the requested expression matrix and metadata, instead of converting the full object.