Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object

Usage

spe2PB(
  spe,
  by.group = TRUE,
  group.id = "cell_type",
  by.roi = TRUE,
  roi.only = TRUE,
  contour = NULL
)

Arguments

spe: A SpatialExperiment object.
by.group: Logical. Whether to perform pseudo-bulking by group. TRUE by default.
group.id: Character. The column name of the colData(spe) that contains the group information. Default to 'cell_type'.
by.roi: Logical. Whether to perform pseudo-bulking by ROI. TRUE by default.
roi.only: Logical. Whether to filter out pseudo-bulk samples formed by cells not in any ROIs. TRUE by default.
contour: Character. The name of the group or cell type on which the contour level is computed. If NULL, then no pseudo-bulking will be performed based on contour level. Default to NULL.

Value

An edgeR::DGEList object where each library (column) is a pseudo-bulk sample.

Examples


data("xenium_bc_spe")

spe <- gridDensity(spe)

coi <- "Breast cancer"

spe <- findROI(spe, coi = coi)

spe <- allocateCells(spe)
#> Assigning cells to ROIs defined by Breast cancer 
#> No contour detected.

y <- spe2PB(spe)