raw_counts_to_feature_count_files: Create a sparse count matrix from various format of input...

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

Description

This function takes three different type of single-cell input: - Single cell BAM files (sorted) - Single cell BED files (gzipped) - A combination of an index file, a peak file and cell barcode file (The index file is composed of three column: index i, index j and value x for the non zeroes entries in the sparse matrix.)

Usage

raw_counts_to_feature_count_files(
  files_dir,
  file_type = c("BAM", "BED", "Index_Peak_Barcode"),
  peak_file = NULL,
  n_bins = NULL,
  bin_width = NULL,
  geneTSS = NULL,
  aroundTSS = 2500,
  verbose = TRUE,
  ref = "hg38"
)

Arguments

files_dir	The directory containing the files
file_type	Input file(s) type(s) ('BAM')
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)
geneTSS	Use geneTSS regions for annotation ? (NULL)
aroundTSS	Space up and downstream of TSS to use (2500)
verbose	Verbose (TRUE)
ref	reference genome to use (hg38)

Details

This functions re-counts signal on either fixed genomic bins, a set of user-defined peaks or around the TSS of genes.

Value

A sparse matrix of features x cells

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