compute_afthreshold: Compute coverage-based and not-coverage-based allelic...
In abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

Description Usage Arguments Value Examples

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

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

`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.

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

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