runDWLSDeconv

runDWLSDeconv

Description

Function to perform DWLS deconvolution based on single cell expression data

Usage

runDWLSDeconv(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized"),
  logbase = 2,
  cluster_column = "leiden_clus",
  sign_matrix,
  n_cell = 50,
  cutoff = 2,
  name = NULL,
  return_gobject = TRUE
)

Arguments

Argument	Description
gobject	giotto object
spat_unit	spatial unit
feat_type	feature type
expression_values	expression values to use
logbase	base used for log normalization
cluster_column	name of cluster column
sign_matrix	sig matrix for deconvolution
n_cell	number of cells per spot
cutoff	cut off (default = 2)
name	name to give to spatial deconvolution results, default = DWLS
return_gobject	return giotto object

Value

giotto object or deconvolution results

Seealso

https://github.com/dtsoucas/DWLS for the DWLS bulk deconvolution method,

and https://doi.org/10.1186/s13059-021-02362-7 for spatialDWLS , the spatial implementation used here.