create.SpaCET.object: Create a SpaCET object

In data2intelligence/SpaCE: Spatial Cellular Estimator for Tumors

Create a SpaCET object

Description

Read an ST dataset to create a SpaCET object.

Usage

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

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.

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.

Value

A SpaCET object.

Examples

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

data2intelligence/SpaCE documentation built on April 17, 2025, 4:23 a.m.