createSCE: Create a SingleCellExperiment Object From Spatial...

In Spaniel: Spatial Transcriptomics Analysis

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)

Spaniel documentation built on Nov. 8, 2020, 5:54 p.m.