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

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

Create a sparse count matrix from various format of input data.

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_sparse_matrix(
  files_dir_list,
  file_type = c("scBED", "scBAM", "FragmentFile"),
  use_Signac = TRUE,
  peak_file = NULL,
  n_bins = NULL,
  bin_width = NULL,
  genebody = NULL,
  extendPromoter = 2500,
  verbose = TRUE,
  ref = c("hg38", "mm10", "ce11")[1],
  progress = NULL,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

files_dir_list	A named character vector of directories containing the files. The names correspond to sample names.
file_type	Input file(s) type(s) ('scBED','scBAM','FragmentFile')
use_Signac	Use Signac wrapper function 'FeatureMatrix' if the Signac package is installed (TRUE).
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)
progress	Progress object for Shiny
BPPARAM	BPPARAM object for multiprocessing. See bpparam for more informations. Will take the default BPPARAM set in your R session.

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

References

Stuart el al., Multimodal single-cell chromatin analysis with Signac bioRxiv https://doi.org/10.1101/2020.11.09.373613

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