SpatialRNA: constructor of SpatialRNA object

In lulizou/spASE: Detecting Allele-Specific 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,
  maternalCounts = NULL,
  paternalCounts = NULL
)

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

Slots

maternalCounts

Optional, for allele specific expression, a matrix (or dgCmatrix) of raw maternal counts for each gene (rowname) and each pixel (colnames or barcodes)

paternalCounts

Optional, for allele specific expression, a matrix (or dgCmatrix) of raw paternal counts for each gene (rowname) and each pixel (colnames or barcodes)

lulizou/spASE documentation built on May 22, 2024, 5:24 a.m.