Read and Load 10x Genomics Xenium in-situ data

Read and Load 10x Genomics Xenium in-situ data

LoadXenium(data.dir, fov = "fov", assay = "Xenium")

ReadXenium(
  data.dir,
  outs = c("matrix", "microns"),
  type = "centroids",
  mols.qv.threshold = 20
)

Arguments

data.dir

Directory containing all Xenium output files with default filenames

fov

FOV name

assay

Assay name

outs

Types of molecular outputs to read; choose one or more of:

• “matrix”: the counts matrix

• “microns”: molecule coordinates

type

Type of cell spatial coordinate matrices to read; choose one or more of:

• “centroids”: cell centroids in pixel coordinate space

• “segmentations”: cell segmentations in pixel coordinate space

mols.qv.threshold

Remove transcript molecules with a QV less than this threshold. QV >= 20 is the standard threshold used to construct the cell x gene count matrix.

Value

LoadXenium: A Seurat object

ReadXenium: A list with some combination of the following values:

• “matrix”: a sparse matrix with expression data; cells are columns and features are rows

• “centroids”: a data frame with cell centroid coordinates in three columns: “x”, “y”, and “cell”

• “pixels”: a data frame with molecule pixel coordinates in three columns: “x”, “y”, and “gene”