Read in Xenium data into a MoleculeExperiment object

Function to read in, and standardise, Xenium output data into an ME object. Detected transcripts files are required. Additionally, it is also possible to read in boundary files ("cell", "nuclei", or both). This function is a wrapper around readMolecules and readBoundaries functions.

Usage

readXenium(dataDir, keepCols = "essential", addBoundaries = "cell")

Arguments

dataDir

Character string specifying the directory with the xenium output files.

keepCols

Vector of characters specifying the columns of interest from the transcripts file and boundaries file. Can be "all" or "essential". "essential" selects columns with gene names, x and y locations in the transcripts file; "essential" selects columns with cell ids, and x and y locations for the vertices defining the boundaries in the boundaries file.

addBoundaries

Vector with which to specify the names of the boundary assays to be added to the me object. Can be "cell", "nucleus", both, or NULL. The latter will lead to the creation of a simple ME object with just the molecules slot filled.

Value

A MoleculeExperiment object containing xenium data.

Examples

repoDir <- system.file("extdata", package = "MoleculeExperiment")
repoDir <- paste0(repoDir, "/xenium_V1_FF_Mouse_Brain")

me <- readXenium(repoDir,
                  keepCols = "essential")
me
#> MoleculeExperiment class
#> 
#> molecules slot (1): detected
#> - detected:
#> samples (2): sample1 sample2
#> -- sample1:
#> ---- features (137): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2
#> ---- molecules (962)
#> ---- location range: [4900,4919.98] x [6400.02,6420]
#> -- sample2:
#> ---- features (143): 2010300C02Rik Acsbg1 ... Zfp536 Zfpm2
#> ---- molecules (777)
#> ---- location range: [4900.01,4919.98] x [6400.16,6419.97]
#> 
#> 
#> boundaries slot (1): cell
#> - cell:
#> samples (2): sample1 sample2
#> -- sample1:
#> ---- segments (5): 67500 67512 67515 67521 67527
#> -- sample2:
#> ---- segments (9): 65043 65044 ... 65070 65071