runSpatialDeconv: runSpatialDeconv

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Function to perform deconvolution based on single cell expression data

Usage

runSpatialDeconv(
  gobject,
  deconv_method = c("DWLS"),
  expression_values = c("normalized"),
  logbase = 2,
  cluster_column = "leiden_clus",
  sign_matrix,
  n_cell = 50,
  cutoff = 2,
  name = NULL,
  return_gobject = TRUE
)

Arguments

gobject	giotto object
deconv_method	method to use for deconvolution
expression_values	expression values to use
logbase	base used for log normalization
cluster_column	name of cluster column
sign_matrix	signature matrix for deconvolution
n_cell	number of cells per spot
cutoff	cut off (default = 2)
name	name to give to spatial deconvolution results
return_gobject	return giotto object

Value

giotto object or deconvolution results

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.