% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/assay5.R
\docType{class}
\name{StdAssay-class}
\alias{StdAssay-class}
\alias{StdAssay}
\title{Core Assay Infrastructure}
\description{
The \code{StdAssay} class is a virtual class that provides core
infrastructure for assay data in \pkg{Seurat}. Assays contain expression
data (layers) and associated feature-level meta data. Derived classes
(eg. \link[=Assay5]{the v5 Assay}) may optionally
define additional functionality
}
\section{Slots}{

\describe{
\item{\code{layers}}{A named list containing expression matrices; each matrix should
be a two-dimensional object containing some subset of cells and features
defined in the \code{cells} and \code{features} slots. Cell and feature
membership is recorded in the \code{cells} and \code{features} slots,
respectively}

\item{\code{cells}}{A \link[=LogMap]{logical mapping} of cell names
and layer membership; this map contains all the possible cells that this
assay can contain. New layers must have some subset of cells present
in this map}

\item{\code{features}}{A \link[=LogMap]{logical mapping} of feature
names and layer membership; this map contains all the possible features that
this assay can contain. New layers must have some subset of features
present in this map}

\item{\code{default}}{A one-length integer with the end index of the
\link[=DefaultLayer]{default layer}; the default layer be
all layers up to and including the layer at index \code{default}}

\item{\code{assay.orig}}{Original assay that this assay is based off of;
used to track assay provenance}

\item{\code{meta.data}}{A \link[base:data.frame]{data frame} with feature-level
meta data; should have the same number of rows as \code{features}}

\item{\code{misc}}{A named list of unstructured miscellaneous data}

\item{\code{key}}{A one-length character vector with the object's key; keys must
be one or more alphanumeric characters followed by an underscore
\dQuote{\code{_}} (regex pattern
\dQuote{\code{\Sexpr[stage=build]{SeuratObject:::.KeyPattern()}}})}
}}

\seealso{
\code{\link{Assay5-class}} \code{\link{Assay5T-class}}

v5 Standard Assay object, validity, and interaction methods
\code{\link{$.StdAssay}()},
\code{\link{.DollarNames.StdAssay}()},
\code{\link{StdAssay-validity}},
\code{\link{[.StdAssay}()},
\code{\link{[[.StdAssay}()},
\code{\link{dim.StdAssay}()},
\code{\link{dimnames.StdAssay}()},
\code{\link{show,StdAssay-method}},
\code{\link{split.StdAssay}()},
\code{\link{subset.StdAssay}()}
}
\concept{stdassay}
\keyword{internal}
