Import and standardize scRNAseq data across different formats

Source: R/ingest_data.R

Automatically infers data format of scRNAseq object, or a path to that object. It then uses the appropriate functions to import that data and convert it to a SingleCellExperiment, which is recognized by other EWCE functions.

ingest_data(
  obj,
  input_type = "guess",
  output_type = "SingleCellExperiment",
  custom_reader = NULL,
  save_dir = tempdir(),
  filename = "scKirby_output",
  save_output = T,
  overwrite = F,
  return_filepath = F,
  verbose = T,
  ...
)

Arguments

obj

Single-cell data object or path to saved single-cell data.
input_type

Format of obj. By default, the type will be inferred.
output_type

Format to convert obj to.
custom_reader

Custom function to read obj into R.
save_dir

Directory to save the converted obj.
filename

Name to save the converted obj.
save_output

Whether or not to save the converted obj.
overwrite

If a file of the same name exists, overwrite it.
return_filepath

If TRUE, a list with both the converted object and the saved file path will be returned (instead of just the converted object).
...

Additional arguments to be passed to scKirby::read_data().

Source

SeuratDisk anndata (R) anndata (python) loomR SingleCellExperiment DelayedArray workshop zellkonverter

Examples