https://github.com/satijalab/seurat
Tip revision: ff03fdf21f1b8fea9ee247d0fd83df5811507027 authored by AustinHartman on 05 December 2022, 22:48:27 UTC
Merge branch 'master' into release/4.3.0
Merge branch 'master' into release/4.3.0
Tip revision: ff03fdf
ReadXenium.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/convenience.R, R/preprocessing.R
\name{LoadXenium}
\alias{LoadXenium}
\alias{ReadXenium}
\title{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{
\item{data.dir}{Directory containing all Xenium output files with
default filenames}
\item{fov}{FOV name}
\item{assay}{Assay name}
\item{outs}{Types of molecular outputs to read; choose one or more of:
\itemize{
\item \dQuote{matrix}: the counts matrix
\item \dQuote{microns}: molecule coordinates
}}
\item{type}{Type of cell spatial coordinate matrices to read; choose one
or more of:
\itemize{
\item \dQuote{centroids}: cell centroids in pixel coordinate space
\item \dQuote{segmentations}: cell segmentations in pixel coordinate space
}}
\item{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{
\code{LoadXenium}: A \code{\link[SeuratObject]{Seurat}} object
\code{ReadXenium}: A list with some combination of the
following values:
\itemize{
\item \dQuote{\code{matrix}}: a
\link[Matrix:dgCMatrix-class]{sparse matrix} with expression data; cells
are columns and features are rows
\item \dQuote{\code{centroids}}: a data frame with cell centroid
coordinates in three columns: \dQuote{x}, \dQuote{y}, and \dQuote{cell}
\item \dQuote{\code{pixels}}: a data frame with molecule pixel coordinates
in three columns: \dQuote{x}, \dQuote{y}, and \dQuote{gene}
}
}
\description{
Read and Load 10x Genomics Xenium in-situ data
}
\concept{preprocessing}