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 )
dir | A character indicates the directory of the 10X files |
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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 |
a SingleCellExperiment object
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 }