import_count_input_files {ChromSCape}R Documentation

Import and count input files depending on their format

Description

Import and count input files depending on their format

Usage

import_count_input_files(
  files_dir,
  file_type,
  which,
  ref,
  peak_file_2,
  barcode_file,
  index_file,
  verbose
)

Arguments

files_dir

Path to the input files

file_type

Input file type

which

A GRanges object of features

ref

Reference genome

peak_file_2

A bed file for peak annotation

barcode_file

A file containing barcode names

index_file

A file containing indexes of non zero entries

verbose

Print ?

Value

A list with a GRanges object of feature types (which), the feature indexes data.frame containing non-zeroes entries in the count matrix and the cell names


[Package ChromSCape version 1.0.0 Index]