getExpression: Get expression values

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Get expression values

Description

Function to get expression values from giotto object

Usage

getExpression(
  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

exprObj or matrix depending on output param

See Also

Other expression accessor functions: setExpression(), set_expression_values()

Other functions to get data from giotto object: getDimReduction(), getFeatureInfo(), getGiottoImage(), getMultiomics(), getNearestNetwork(), getPolygonInfo(), getSpatialEnrichment(), getSpatialGrid(), getSpatialLocations(), getSpatialNetwork(), get_NearestNetwork(), get_dimReduction(), get_feature_info(), get_giottoImage(), get_multiomics(), get_polygon_info(), get_spatialGrid(), get_spatialNetwork(), get_spatial_enrichment(), get_spatial_locations()

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.