Create a SpaCET object — create.SpaCET.object • SpaCET

Read an ST dataset to create a SpaCET object.

Usage

create.SpaCET.object(
  counts,
  spotCoordinates,
  metaData = NULL,
  imagePath = NA,
  platform,
  organism = "human"
)

Arguments

counts: Count matrix with gene name (row) x spot ID (column).
spotCoordinates: Spot coordinate matrix with spot ID (row) x coordinates (column). This matrix should include two columns, i,e., X and Y coordinates, respectively, which represent the position of spots in H&E image.
imagePath: Path to the H&E image file. Can be NA if it is not available.
platform: A character string indicating the platform, i.e., "Visium", "OldST", or "Slide-Seq". "OldST" is the early in situ capturing method from which "Visium" was developed.
organism: Organism of the sample, e.g., human or mouse.

Value

A SpaCET object.

Details

To create a SpaCET object, user need to input four parameters, i.e., "counts", "spotCoordinates", "imagePath", and "platform". However, if analyzing the Visium data, it is more easy to use `create.SpaCET.object.10X` to read ST data.

Examples

SpaCET_obj <- create.SpaCET.object(counts, spotCoordinates, imagePath, platform)