% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/importFromFiles.R
 \name{importFromFiles}
 \alias{importFromFiles}
 \title{Create a SingleCellExperiment object from files}
 \usage{
 importFromFiles(
   assayFile,
   annotFile = NULL,
   featureFile = NULL,
   assayName = "counts",
   inputDataFrames = FALSE,
   class = c("Matrix", "matrix"),

   delayedArray = FALSE,
   annotFileHeader = FALSE,
   annotFileRowName = 1,
   annotFileSep = "\\t",
   featureHeader = FALSE,
   featureRowName = 1,
   featureSep = "\\t",

   gzipped = "auto",
   rowNamesDedup = TRUE

 )
 }
 \arguments{

 \item{assayFile}{The path to a file in .mtx, .txt, .csv, .tab, or .tsv 
 format.}

 
 \item{annotFile}{The path to a text file that contains columns of annotation

 information for each cell in the \code{assayFile}. This file should have the 
 same number of rows as there are columns in the \code{assayFile}. If multiple
 samples are represented in the dataset, this should be denoted by a column 
 called \code{'sample'} within the \code{annotFile}.}

 
 \item{featureFile}{The path to a text file that contains columns of
 annotation information for each gene in the count matrix. This file should

 have the same genes in the same order as \code{assayFile}. This is optional.}

 
 \item{assayName}{The name of the assay that you are uploading. The default

 is \code{"counts"}.}

 \item{inputDataFrames}{If \code{TRUE}, \code{assayFile}, \code{annotFile} and
 \code{featureFile} should be \code{data.frames} object (or its inheritance) 
 instead of file paths. The default is \code{FALSE}.}

 
 \item{class}{Character. The class of the expression matrix stored in the SCE

 object. Can be one of \code{"Matrix"} (as returned by
 \link{readMM} function), or \code{"matrix"} (as returned by
 \link[base]{matrix} function). Default \code{"Matrix"}.}

 
 \item{delayedArray}{Boolean. Whether to read the expression matrix as

 \link{DelayedArray} object or not. Default \code{FALSE}.}

 \item{annotFileHeader}{Whether there's a header (colnames) in the cell 
 annotation file. Default is \code{FALSE}.}

 \item{annotFileRowName}{Which column is used as the rownames for the cell 
 annotation file. This should match to the colnames of the \code{assayFile}. 
 Default is \code{1} (first column).}

 \item{annotFileSep}{Separater used for the cell annotation file. Default is 
 \code{"\\t"}.}

 \item{featureHeader}{Whether there's a header (colnames) in the feature 
 annotation file. Default is \code{FALSE}.}

 \item{featureRowName}{Which column is used as the rownames for the feature 
 annotation file. This should match to the rownames of the \code{assayFile}. 
 Default is \code{1}. (first column).}

 \item{featureSep}{Separater used for the feature annotation file. Default is 
 \code{"\\t"}.}

 \item{gzipped}{Whether the input file is gzipped. Default is \code{"auto"} 
 and it will automatically detect whether the file is gzipped. Other options 
 are \code{TRUE} or \code{FALSE}.}
 
 \item{rowNamesDedup}{Boolean. Whether to deduplicate rownames. Default 
 \code{TRUE}.}

 }
 \value{

 a \linkS4class{SingleCellExperiment} object

 }
 \description{

 Create a SingleCellExperiment object from files
 }
 \details{
 Creates a \linkS4class{SingleCellExperiment} object from a counts 
 file in various formats, and files of cell and feature annotation.

 }