Bin atac fragments — bin_atac

Convenience wrapper to bin fragments of a given size and save them as .mtx files

Usage

bin_atac_frags(
  sample_id,
  fragment_file,
  cells = NULL,
  bins,
  bin_name = NULL,
  blacklist = NULL,
  outdir,
  ncores = 1,
  bpparam = BiocParallel::SerialParam(),
  overwrite = FALSE,
  return_mat = FALSE
)

Arguments

sample_id: Sample id
fragment_file: Fragments file
cells: A vector of cell barcodes. If not provided will use all barcodes
bins: Genomic ranges object with bins to use
bin_name: bin_name Name of the bins (e.g. '10Mb', '500Kb', 'chr_arm'). If not provided is automatically detected based on binwidth.
blacklist: Genome blacklist regions to filter against
outdir: Output directory
ncores: Number of cores
bpparam: BiocParallel Parameters
overwrite: Whether to overwrite previous binned counts
return_mat: Logical. Return the binned depth matrix (default = FALSE)

Value

If return_mat=TRUE, returns a sparse binned depth matrix. Otherwise returns NULL, but will save the results to a 10X style market matrix outdir