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