A function to read the data from 10X

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

if (FALSE) { 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 }