makeSignMatrixDWLS: makeSignMatrixDWLS

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

makeSignMatrixDWLS

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.