% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/SingleCellAssay-methods.R

\name{FromMatrix}

\alias{FromMatrix}

\title{Construct a SingleCellAssay from a matrix or array of expression}

\usage{

FromMatrix(

exprsArray,

cData,

fData,

class = "SingleCellAssay",

check_sanity = TRUE,

check_logged = check_sanity

)

}

\arguments{

\item{exprsArray}{matrix, or a list of matrices, or an array. Columns are cells, rows are genes.}

\item{cData}{cellData an object that can be coerced to a DataFrame, ie, data.frame, AnnotatedDataFrame. Must have as many rows as \code{ncol(exprsArray)}}

\item{fData}{featureData an object that can be coerced to a DataFrame, ie, data.frame, AnnotatedDataFrame. Must have as many rows as \code{nrow(exprsArray)}.}

\item{class}{desired subclass of object. Default \code{SingleCellAssay}.}

\item{check_sanity}{(default: \code{TRUE}) Set \code{FALSE} to override sanity checks that try to ensure that the default assay is log-transformed and has at least one exact zero. See \link{defaultAssay} for details on the "default assay" which is assumed to contain log transformed data.}

\item{check_logged}{alias for \code{check_sanity}}

}

\value{

an object of class \code{class}

}

\description{

If the gene expression measurements are already in a rectangular form,

then this function allows an easy way to construct a SingleCellAssay object while

still doing some sanity checking of inputs.

}

\examples{

ncells <- 10

ngenes <- 5

fData <- data.frame(primerid=LETTERS[1:ngenes])

cData <- data.frame(wellKey=seq_len(ncells))

mat <- matrix(rnorm(ncells*ngenes), nrow=ngenes)

sca <- FromMatrix(mat, cData, fData)

stopifnot(inherits(sca, 'SingleCellAssay'))

stopifnot(inherits(sca, 'SummarizedExperiment'))

cData$ncells <- 1

fd <- FromMatrix(mat, cData, fData)

stopifnot(inherits(fd, 'SingleCellAssay'))

}

\seealso{

}