createSCE {Spaniel} | R Documentation |
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.
createSCE(counts, barcodeFile, projectName=projectName, sectionNumber=sectionNo)
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 |
A SingleCellExeriment Object
## 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)