compute_afthreshold: Compute coverage-based and not-coverage-based allelic...

In cibiobcg/abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

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

outdir <- tempdir()
pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
outafth <- compute_afthreshold(outdir = outdir,pbem_dir = pbem_dir)

cibiobcg/abemus documentation built on Oct. 29, 2022, 9:03 p.m.