Create a SpaCET object from 10X Genomics platforms — create.SpaCET.object.10X • SpaCET

Read an ST dataset to create a SpaCET object.

Usage

create.SpaCET.object.10X(
  dataPath = NULL,
  visiumPath = NULL,
  platform = "Visium",
  organism = "human"
)

Arguments

dataPath: Path to a Visium, Visium HD, or Xenium output directory. See Details for the directory expected for each platform.
visiumPath: Path to the Space Ranger output folder. This is a deprecated parameter. Please use `dataPath` instead.
platform: A character string indicating the platform, i.e., "Visium", "VisiumHD", or "Xenium".
organism: Organism of the sample, e.g., human or mouse.

Value

A SpaCET object.

Details

The directory supplied through dataPath depends on the platform:

Visium: the Space Ranger output directory.
Binned Visium HD: one binned_outputs/square_*um directory.
Segmented Visium HD: the segmented_outputs directory.
Xenium: the Xenium output directory.

Examples

visiumPath <- file.path(system.file(package = "SpaCET"), "extdata/Visium_BC")
SpaCET_obj <- create.SpaCET.object.10X(dataPath = visiumPath, platform = "Visium", organism="human")