makeSignMatrixDWLS: makeSignMatrixDWLS

In RubD/Giotto: 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. A vector of cell types for cell_type_vector can be created from the cell metadata (pDataDT).

Usage

makeSignMatrixDWLS(
  gobject,
  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
expression_values	expression values to use
reverse_log	reverse a log-normalized expression matrix
log_base	the logarithm base (deafult = 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

spatialDWLS

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.