SpatialRNA: constructor of SpatialRNA object

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

constructor of SpatialRNA object

Description

constructor of SpatialRNA object

Usage

SpatialRNA(
  coords,
  counts,
  nUMI = NULL,
  use_fake_coords = FALSE,
  require_int = TRUE
)

Arguments

coords	A data.frame (or matrix) representing the spatial pixel locations. rownames are barcodes/pixel names, and there should be two columns for 'x' and for 'y'.
counts	A matrix (or dgCmatrix) representing Digital Gene Expression (DGE). Rownames should be genes and colnames represent barcodes/pixel names.
nUMI	Optional, a named (by pixel 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.
use_fake_coords	logical, FALSE by default. If true, the 'coords' parameter will be ignored, and replaced with a placeholder coords matrix.
require_int	logical, TRUE by default. If true, requires counts and nUMI to be integers. Counts should be untransformed count-level data

Value

Returns a SpatialRNA object containing the coordinates and counts from the input files

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