Skip to contents

Build the ambient contamination field

Source: R/AllGenerics.R, R/paceFit.R
ambientField.Rd

Returns the sparse cross-cell-type ambient weight matrix that defines the per-cell contamination term (the short-range technical field a cell receives from its heterotypic neighbours).

Usage

ambientField(object, ...)

# S4 method for class 'SpatialExperiment'
ambientField(
  object,
  celltype_col,
  image_col = NULL,
  h_tech = 5,
  assay_name = "counts",
  ...
)

Arguments

object

A SpatialExperiment::SpatialExperiment.

...

Passed to the ambient-field builder.

celltype_col

colData column with the cell-type annotation.

image_col

Optional colData column grouping cells into images.

h_tech

Technical bandwidth in micrometres (default 5).

assay_name

Counts assay name (default "counts").

Value

The ambient-field object (sparse weight matrix and image index).

Examples

spe <- readRDS(system.file("extdata", "bc_xenium_subset.rds", package = "PACE"))
af <- ambientField(spe, celltype_col = "cellType")
#>     [W identity check] max|W%*%Y - dense E_tech| over 5 genes = 8.882e-16
names(af)
#> [1] "W"         "image_idx" "n_images"