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get_expression_values

Source: R/slot_accessors.R
get_expression_values.Rd

get_expression_values

Usage

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

Arguments

gobject

giotto object

spat_unit

spatial unit (e.g. "cell")

feat_type

feature type (e.g. "rna", "dna", "protein")

values

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

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