abemus (version 1.0.2)

compute_afthreshold: Compute coverage-based and not-coverage-based allelic fraction thresholds

Description

Compute coverage-based and not-coverage-based allelic fraction thresholds

Usage

compute_afthreshold(outdir, pbem_dir = file.path(outdir,
  "BaseErrorModel"), outdir.afth.name = "Controls",
  coverage_binning = 50, probs = seq(0.9, 1, 1e-04))

Arguments

outdir

The folder where outputs will be saved.

pbem_dir

The folder with outputs generated by the compute_pbem function. default: file.path(outdir, "BaseErrorModel")

outdir.afth.name

The subfolder name that will be created in the outdir. default: "Controls"

coverage_binning

Bins of coverage into which divide AFs. default: 50

probs

Quantiles dividing the distribution of allelic fractions.

Value

A matrix with allelic fraction thresholds. Rows are quantiles as set by probs and columns are coverage bins as set by coverage_binning

Examples

# NOT RUN {
outdir <- tempdir()
pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
outafth <- compute_afthreshold(outdir = outdir,pbem_dir = pbem_dir)
# }