warning_raw_counts_to_sparse_matrix: Warning for raw_counts_to_sparse_matrix

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

Warning for raw_counts_to_sparse_matrix

Description

Warning for raw_counts_to_sparse_matrix

Usage

warning_raw_counts_to_sparse_matrix(
  files_dir_list,
  file_type = c("scBAM", "scBED", "SparseMatrix"),
  peak_file = NULL,
  n_bins = NULL,
  bin_width = NULL,
  genebody = NULL,
  extendPromoter = 2500,
  verbose = TRUE,
  ref = "hg38"
)

Arguments

files_dir_list	A named character vector of directory containing the raw files
file_type	Input file(s) type(s) ('scBED','scBAM','SparseMatrix')
peak_file	A file containing genomic location of peaks (NULL)
n_bins	The number of bins to tile the genome (NULL)
bin_width	The size of bins to tile the genome (NULL)
genebody	Count on genes (body + promoter) ? (NULL)
extendPromoter	If counting on genes, number of base pairs to extend up or downstream of TSS (2500).
verbose	Verbose (TRUE)
ref	reference genome to use (hg38)

Value

Error or warnings if the input are not correct

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.