runDWLSDeconv#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_enrichment.R#L1817

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 list(“DWLS?) bulk deconvolution method, and c(“\Sexpr[results=rd]{tools:::Rd_expr_doi(“#1”)}?, “10.1186/s13059-021-02362-7?) list(“tools:::Rd_expr_doi(“10.1186/s13059-021-02362-7”)?) for list(“spatialDWLS?) , the spatial implementation used here.