Get expression values#

Last Updated: Sep 07, 2023

Description#

Function to get expression values from giotto object

Usage#

get_expression_values(
  gobject,
  values = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  output = c("exprObj", "matrix"),
  set_defaults = TRUE
)

Arguments#

gobject

giotto object

values

expression values to extract (e.g. “raw”, “normalized”, “scaled”)

spat_unit

spatial unit (e.g. “cell”)

feat_type

feature type (e.g. “rna”, “dna”, “protein”)

output

what object type to retrieve the expression as. Currently either ‘matrix’ for the matrix object contained in the exprObj or ‘exprObj’ (default) for the exprObj itself are allowed.

set_defaults

set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.

Value#

expression matrix

See Also#

Other expression accessor functions: set_expression_values()

Other functions to get data from giotto object: get_NearestNetwork(), get_dimReduction(), get_feature_info(), get_giottoImage(), get_polygon_info(), get_spatialGrid(), get_spatialNetwork(), get_spatial_enrichment(), get_spatial_locations()