LoadXenium {Seurat}R Documentation

Read and Load 10x Genomics Xenium in-situ data

Description

Read and Load 10x Genomics Xenium in-situ data

Usage

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:


[Package Seurat version 5.1.0 Index]