Run fragtk matrix — RunFragtk • Signac

Wrapper function to run fragtk matrix and return the output as a sparse matrix in R.

Usage

RunFragtk(
  fragments,
  features,
  cells,
  group = FALSE,
  pic = TRUE,
  fragtk.path = NULL,
  outdir = tempdir(),
  cleanup = TRUE,
  verbose = TRUE
)

Arguments

fragments: A list of Fragment objects or fragment file paths
features: A GRanges object containing a set of genomic intervals to quantify. These genomic ranges will be passed to the --bed argument in fragtk matrix
cells: List of cells to include
group: Group genomic ranges according to a grouping variable. If NULL, no grouping variable is used. If a character string is provided, this should match a column in the provided GRanges object supplied in the features parameter.
pic: Use paired insertion counting
fragtk.path: Path to fragtk executable. If NULL, try to find fragtk automatically.
outdir: Path for output directory
cleanup: Remove output files created by fragtk
verbose: Display messages

Value

Returns a CsparseMatrix

Details

See https://crates.io/crates/fragtk for fragtk documentation.