makeSignMatrixDWLS#

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Last Updated: Mar 11, 2023

Description#

Function to convert a matrix within a Giotto object into a format that can be used with runDWLSDeconv for deconvolution. A vector of cell types for parameter cell_type_vector can be created from the cell metadata (pDataDT).

Usage#

makeSignMatrixDWLS(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  reverse_log = TRUE,
  log_base = 2,
  sign_gene,
  cell_type_vector,
  cell_type = NULL
)

Arguments#

`gobject`	Giotto object of single cell
`spat_unit`	spatial unit
`feat_type`	feature type to use
`expression_values`	expression values to use
`reverse_log`	reverse a log-normalized expression matrix
`log_base`	the logarithm base (default = 2)
`sign_gene`	all of DE genes (signature)
`cell_type_vector`	vector with cell types (length = ncol(matrix))
`cell_type`	deprecated, use `cell_type_vector`

Value#

matrix

See Also#

runDWLSDeconv