import_count_input_files: Import and count input files depending on their format

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

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

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.