Create an SpaCET object

Read an ST dataset to create an SpaCET object.

Usage

create.SpaCET.object(counts, spotCoordinates, imagePath, 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.

Value

An SpaCET object.

Details

To create an 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)