createSeurat: Create a Seurat Object From Spatial Transcriptomics Data

Description Usage Arguments Value Examples

View source: R/readData.R

Description

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

Usage

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createSeurat(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 Seurat Object

Examples

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## 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")
SeuratObj <- createSeurat(examplecounts,
                        exampleBarcodes,
                        projectName = "TestProj",
                        sectionNumber = 1
                        )

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