View source: R/preprocessing.R
LoadXenium | R Documentation |
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
)
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. |
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”
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