Build a WisecondorX reference panel

Calls wisecondorx newref via condathis::run() on a set of NPZ files produced by bam_convert_npz(). The NPZ files must all use the same binsize; the reference is built at ref_binsize (must be a multiple of binsize).

Usage

wisecondorx_newref(
  npz_files,
  output,
  binsize = 5000L,
  ref_binsize = 100000L,
  nipt = FALSE,
  refsize = 300L,
  yfrac = NULL,
  plotyfrac = NULL,
  cpus = 1L,
  env_name = "wisecondorx",
  extra_args = character(0)
)

Arguments

npz_files

Character vector of paths to .npz files (one per sample).

output

Path for the output reference .npz file.

binsize

Convert-step bin size in base pairs (default 5000). Must match the binsize used when calling bam_convert_npz().

ref_binsize

Reference bin size in base pairs (default 100000). Passed to upstream --binsize. Must be a multiple of binsize.

nipt

Logical; pass upstream --nipt.

refsize

Number of reference locations per target bin. Passed to upstream --refsize.

yfrac

Optional numeric Y-read fraction cutoff. Passed to upstream --yfrac.

plotyfrac

Optional output path for the Y-fraction histogram and mixture-model plot. Passed to upstream --plotyfrac.

cpus

Number of CPUs to pass to wisecondorx newref (default 1).

env_name

Name of the conda environment containing wisecondorx (default "wisecondorx"). Created automatically by condathis on first use via the bioconda channel.

extra_args

Character vector of additional arguments passed verbatim after the mapped CLI flags. Keep this for forward compatibility with future upstream WisecondorX releases.

Value

output (invisibly).

Details

This wrapper exposes the current upstream wisecondorx newref CLI flags documented in the WisecondorX README: --nipt, --binsize, --refsize, --yfrac, --plotyfrac, and --cpus.

See also

bam_convert_npz(), wisecondorx_predict()

Examples

if (FALSE) { # \dontrun{
wisecondorx_newref(
  npz_files = list.files("controls/", "\\.npz$", full.names = TRUE),
  output = "reference.npz",
  binsize = 5000L,
  ref_binsize = 100000L,
  nipt = TRUE,
  refsize = 300L,
  yfrac = 0.05,
  cpus = 1L
)
} # }