Reference: constructor of 'Reference' object

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

constructor of Reference object

Description

constructor of Reference object

Usage

Reference(
  counts,
  cell_types,
  nUMI = NULL,
  require_int = TRUE,
  n_max_cells = 10000,
  min_UMI = 100
)

Arguments

counts	A matrix (or dgCmatrix) representing Digital Gene Expression (DGE). Rownames should be genes and colnames represent barcodes/cell names.
cell_types	A named (by cell barcode) factor of cell type for each cell. The 'levels' of the factor would be the possible cell type identities.
nUMI	Optional, a named (by cell barcode) list of total counts or UMI's appearing at each pixel. If not provided, nUMI will be assumed to be the total counts appearing on each pixel.
n_max_cells	(default 10,000) the maximum number of cells per cell type. Will downsample if this number is exceeded. Counts should be untransformed count-level data
min_UMI	(default 100) minimum UMI count for cells to be included in the reference.

Value

Returns a Reference object containing the counts matrix, cell type labels, and UMI vector from the input files

dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.