% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/QCfunctions.R
 \name{readFrom10X}
 \alias{readFrom10X}

 \title{readFrom10X}

 \usage{
 readFrom10X(
   dir,
   type = c("auto", "sparse", "HDF5"),
   feature_named_by = c("gene_id", "gene_symbol"),
   filter_features = TRUE
 )
 }
 \arguments{
 \item{dir}{A character indicates the directory of the 10X files}
 
 \item{type}{A character indicates the format of the data, sparse or HDF5}
 

 \item{feature_named_by}{A character indicates whehter the genes
 will be named by gene_id or gene_symbol}

 \item{filter_features}{A logical input indicates whether the features
 with all zeros will be removed}

 }

 \value{
 a SingleCellExperiment object
 }

 \description{
 A function to read the data from 10X
 }

 \examples{
 

 \dontrun{

 tmpdir <- tempdir()
 tenXdata <- "http://cf.10xgenomics.com/samples/cell-exp/3.1.0/connect_5k_pbmc_NGSC3_ch1/"
 file <- "connect_5k_pbmc_NGSC3_ch1_filtered_feature_bc_matrix.tar.gz"
 download.file(paste0(tenXdata, file),file.path(tmpdir, file))
 untar(file.path(tmpdir,file),
       exdir = tmpdir)
 sce_citeseq_10X <- readFrom10X(file.path(tmpdir,
 "filtered_feature_bc_matrix/"))
 sce_citeseq_10X

 }

 
 }