raw_counts_to_sparse_matrix {ChromSCape} | R Documentation

## 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")[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

[Package ChromSCape version 1.2.62 Index]