% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/assay.R
\name{CreateAssayObject}
\alias{CreateAssayObject}
\title{Create an Assay object}
\usage{
CreateAssayObject(
  counts,
  data,
  min.cells = 0,
  min.features = 0,
  key = NULL,
  check.matrix = FALSE,
  ...
)
}
\arguments{
\item{counts}{Unnormalized data such as raw counts or TPMs}

\item{data}{Prenormalized data; if provided, do not pass \code{counts}}

\item{min.cells}{Include features detected in at least this many cells. Will
subset the counts matrix as well. To reintroduce excluded features, create a
new object with a lower cutoff}

\item{min.features}{Include cells where at least this many features are
detected}

\item{key}{Optional key to initialize assay with}

\item{check.matrix}{Check counts matrix for NA, NaN, Inf, and
non-integer values}

\item{...}{Arguments passed to \code{\link{as.sparse}}}
}
\value{
A \code{\link{Assay}} object
}
\description{
Create an Assay object from a feature (e.g. gene) expression matrix. The
expected format of the input matrix is features x cells.
}
\details{
Non-unique cell or feature names are not allowed. Please make unique before
calling this function.
}
\examples{
\dontrun{
pbmc_raw <- read.table(
  file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'),
  as.is = TRUE
)
pbmc_rna <- CreateAssayObject(counts = pbmc_raw)
pbmc_rna
}

}
\seealso{
v3 Assay object, validity, and interaction methods:
\code{\link{$.Assay}()},
\code{\link{Assay-class}},
\code{\link{Assay-validity}},
\code{\link{[.Assay}()},
\code{\link{[[.Assay}()},
\code{\link{dim.Assay}()},
\code{\link{dimnames.Assay}()},
\code{\link{merge.Assay}()},
\code{\link{split.Assay}()},
\code{\link{subset.Assay}()}
}
\concept{assay}
