Predict copy-number aberrations with WisecondorX

Calls wisecondorx predict via condathis::run() on a single-sample NPZ file against a reference panel built by wisecondorx_newref().

Usage

wisecondorx_predict(
  npz,
  ref,
  output_prefix,
  minrefbins = 150L,
  maskrepeats = 5L,
  zscore = 5,
  alpha = 1e-04,
  beta = NULL,
  blacklist = NULL,
  gender = NULL,
  bed = FALSE,
  plot = FALSE,
  regions = NULL,
  ylim = NULL,
  cairo = FALSE,
  seed = NULL,
  add_plot_title = FALSE,
  env_name = "wisecondorx",
  extra_args = character(0)
)

Arguments

npz

Path to the sample .npz file (from bam_convert_npz()).

ref

Path to the reference .npz file (from wisecondorx_newref()).

output_prefix

Output prefix for all wisecondorx predict output files (e.g. "results/sample1").

minrefbins

Minimum number of sensible reference bins per target bin. Passed to upstream --minrefbins.

maskrepeats

Number of repeat-masking cycles. Passed to upstream --maskrepeats.

zscore

Z-score threshold for aberration calling. Passed to upstream --zscore.

alpha

P-value cutoff for circular binary segmentation breakpoints. Passed to upstream --alpha.

beta

Optional ratio cutoff for aberration calling. Passed to upstream --beta. When set, upstream ignores zscore.

blacklist

Optional path to a headerless BED blacklist file. Passed to upstream --blacklist.

gender

Optional forced gender, "F" or "M". Passed to upstream --gender.

bed

Logical; also write BED output files. Passed to upstream --bed.

plot

Logical; also write plot output files. Passed to upstream --plot.

regions

Optional path to a headerless BED file with regions to mark on the plot. Passed to upstream --regions.

ylim

Optional numeric vector of length 2 giving the y-axis interval, e.g. c(-2, 2). Passed to upstream --ylim as [a,b].

cairo

Logical; use Cairo bitmap output. Passed to upstream --cairo.

seed

Optional integer random seed for segmentation. Passed to upstream --seed.

add_plot_title

Logical; when TRUE, adds the output basename as the plot title. Passed to upstream --add-plot-title. Only effective when plot = TRUE.

env_name

Name of the conda environment containing wisecondorx (default "wisecondorx").

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_prefix (invisibly).

Details

This wrapper exposes the current upstream wisecondorx predict CLI flags documented in the WisecondorX README: --minrefbins, --maskrepeats, --zscore, --alpha, --beta, --blacklist, --gender, --bed, --plot, --add-plot-title, --regions, --ylim, --cairo, and --seed.

See also

bam_convert_npz(), wisecondorx_newref()

Examples

if (FALSE) { # \dontrun{
wisecondorx_predict(
  npz = "sample.npz",
  ref = "reference.npz",
  output_prefix = "results/sample",
  minrefbins = 150L,
  maskrepeats = 5L,
  zscore = 5,
  alpha = 1e-4,
  beta = NULL,
  blacklist = NULL,
  gender = "F",
  bed = TRUE,
  plot = TRUE,
  add_plot_title = TRUE,
  regions = NULL,
  ylim = c(-2, 2),
  cairo = FALSE,
  seed = 1L
)
} # }