Read a umi_tools count table — read_umi

read_umi_tools() reads a (optionally gzipped) tab-separated condensed count matrix from umi_tools, with the columns gene, cell and count, into an AnnData() object with a sparse (CSR) X, as Python's read_umi_tools(). The obs and var names are the sorted unique cells and genes (Python's category order), with the index names "cell" and "gene". Repeated cell and gene pairs are summed and other columns are ignored.

Usage

read_umi_tools(filename, dtype = NULL)

Arguments

filename: A path (a .gz or .bz2 suffix is decompressed).
dtype: A numpy dtype string for X, such as "float32". With NULL the dtype of the counts is used ("int64" for whole numbers, otherwise "float64").

Value

An AnnData() object with a sparse (CSR) X.

Examples

path <- tempfile(fileext = ".tsv")
writeLines(
  c("gene\tcell\tcount", "g2\tc2\t3", "g1\tc1\t1", "g3\tc1\t2"),
  path
)
read_umi_tools(path)
#> AnnData object with n_obs × n_vars = 2 × 3
#>     layers: None (.X)