Import and count input files depending on their format

Source: R/preprocessing_filtering_reduction.R

Import and count input files depending on their format

import_count_input_files(
  files_dir_list,
  file_type,
  which,
  ref,
  verbose,
  progress,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

files_dir_list

A named list of directories containing the input files.
file_type

Input file type.
which

A GRanges object of features.
ref

Reference genome.
verbose

Print ?
progress

A progress object for Shiny.
BPPARAM

BPPARAM object for multiprocessing. See bpparam for more informations. Will take the default BPPARAM set in your R session.

Value

A list with the feature indexes data.frame containing non-zeroes entries in the count matrix and the cell names