readFrom10X: readFrom10X

In SydneyBioX/CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

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)

SydneyBioX/CiteFuse documentation built on Feb. 13, 2023, 6:04 a.m.