Write single cell counts from a 10x fragments file — scc_from

This function writes an ScCounts object from a "fragments.tsv.gz" which is an output of the 10x pipeline ("Barcoded and aligned fragment file").

Usage

scc_from_fragments(
  fragments_file,
  out_dir,
  cell_names,
  cell_suffix = NULL,
  genome = NULL,
  bin_size = 50000000,
  overwrite = FALSE,
  id = "",
  description = "",
  verbose = FALSE,
  tabix_bin = "tabix",
  chromosomes = gintervals.all()$chrom
)

write_sc_counts_from_fragments(
  fragments_file,
  out_dir,
  cell_names,
  cell_suffix = NULL,
  genome = NULL,
  bin_size = 50000000,
  overwrite = FALSE,
  id = "",
  description = "",
  verbose = FALSE,
  tabix_bin = "tabix",
  chromosomes = gintervals.all()$chrom
)

Arguments

fragments_file: path to fragments file. Note that in order to use tabix, the file must be compressed with gzip and have a ".gz" extension.
out_dir: output directory.
cell_names: a vector with the cell names or an ScPeaks object
cell_suffix: a suffix to add to the cell names (optional). This is useful when you want to merge multiple batches of cells. The suffix would be added in the following way: paste0(cell_name, "-", cell_suffix).
bin_size: Size of the genomic bins to use (in bp). Each chromsome will be chunked into bins with size which is smaller than this value. Default is 50Mb.
overwrite: overwrite existing directory (optional)
id: an identifier for the object, e.g. "pbmc".
description: description of the object, e.g. "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)"
verbose: verbose output (optional)
tabix_bin: path to the tabix binary (optional)
chromosomes: process only specific chromosomes (optional).

Value

None

Examples

if (FALSE) {
scc_from_fragments("pbmc_data/fragments.tsv.gz", "pbmc_reads", cell_names = atac_sc)
scc_from_fragments("pbmc_data/fragments.tsv.gz", "pbmc_reads", cell_names = atac_sc, chromosomes = paste0("chr", c(1:22, "X", "Y")))
}