readFrom10X {CiteFuse} | R Documentation

## readFrom10X

### Description

A function to read the data from 10X

### Usage

    readFrom10X(
      dir,
      type = c("auto", "sparse", "HDF5"),
      feature_named_by = c("gene_id", "gene_symbol"),
      filter_features = TRUE
    )

### Arguments

`dir` | A character indicates the directory of the 10X files
`type` | A character indicates the format of the data, sparse or HDF5
`feature_named_by` | A character indicates whehter the genes will be named by gene_id or gene_symbol
`filter_features` | A logical input indicates whether the features with all zeros will be removed

### Value

a SingleCellExperiment object

### Examples

    ## Not run:
    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

    ## End(Not run)

[Package CiteFuse version 1.2.1 Index]