% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/importAlevin.R
 \name{importAlevin}
 \alias{importAlevin}
 \title{Construct SCE object from Salmon-Alevin output}
 \usage{

 importAlevin(
   alevinDir = NULL,
   sampleName = "sample",
   delayedArray = FALSE,

   class = c("Matrix", "matrix"),
   rowNamesDedup = TRUE

 )

 }
 \arguments{

 \item{alevinDir}{Character. The output directory of salmon-Alevin pipeline.

 It should contain subfolder named 'alevin', which contains the count data
 which is stored

 in 'quants_mat.gz'. Default \code{NULL}.}
 
 \item{sampleName}{Character. A user-defined sample name for the sample to be

 imported. The 'sampleName' will be appended to the begining of cell
 barcodes. Default is 'sample'.}

 
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
 \link{DelayedArray} object or not. Default \code{FALSE}.}

 
 \item{class}{Character. The class of the expression matrix stored in the SCE
 object. Can be one of "Matrix" (as returned by
 \link{readMM} function), or "matrix" (as returned by
 \link[base]{matrix} function). Default "Matrix".}

 
 \item{rowNamesDedup}{Boolean. Whether to deduplicate rownames. Default 
 \code{TRUE}.}

 }
 \value{
 A \code{SingleCellExperiment} object containing the count

  matrix, the feature annotations, and the cell annotation

  (which includes QC metrics stored in 'featureDump.txt').
 }
 \description{
 Construct SCE object from Salmon-Alevin output
 }