createSCE {Spaniel} | R Documentation

## Create a SingleCellExperiment Object From Spatial Transcriptomics Data

### Description

This function converts a count matrix into a SingleCellExperiment object. The barcodes for each spot are added to the coldata of the SingleCellExperiment object and are used in plotting the data.

### Usage

    createSCE(counts, barcodeFile, projectName=projectName,
                    sectionNumber=sectionNo)

### Arguments

`counts` | Raw count matrix or data frame where each row represents a gene and each column represents barcoded location on a spatial transcriptomics slide. The columns should be named using the spot barcode (eg "GTCCGATATGATTGCCGC")
`barcodeFile` | a tab seperated barcode file supplied by Spatial Trancscriptomics. The file should contains three column: The first column contains the Spatial Transcriptomics barcode, the second and third column equate to the x and y location
`projectName` | The name of the project which is stored in the Seurat Object.
`sectionNumber` | The location of the sample on the slide

### Value

A SingleCellExeriment Object

### Examples

    ## Data is taken from DOI: 10.1126/science.aaf2403
    examplecounts <- readRDS(file.path(system.file(package = "Spaniel"),
                                "extdata/counts.rds"))
    exampleBarcodes <- file.path(system.file(package = "Spaniel"),
                                "1000L2_barcodes.txt")
    seuratOb <- createSCE(examplecounts,
                            exampleBarcodes,
                            projectName = "TestProj",
                            sectionNumber = 1)

[Package Spaniel version 1.2.0 Index]