vanquish: Variant Quality Investigation Helper

Imports Variant Calling Format file into R. It can detect whether a sample contains contaminant from the same species. In the first stage of the approach, a change-point detection method is used to identify copy number variations for filtering. Next, features are extracted from the data for a support vector machine model. For log-likelihood calculation, the deviation parameter is estimated by maximum likelihood method. Using a radial basis function kernel support vector machine, the contamination of a sample can be detected.

Version: 1.0.0
Depends: R (≥ 3.4.0)
Imports: changepoint, e1071, ggplot2, stats, VGAM
Published: 2018-09-05
Author: Tao Jiang [aut, cre]
Maintainer: Tao Jiang <tjiang8 at>
License: GPL-2
NeedsCompilation: no
Materials: README
CRAN checks: vanquish results


Reference manual: vanquish.pdf


Package source: vanquish_1.0.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): vanquish_1.0.0.tgz, r-oldrel (arm64): vanquish_1.0.0.tgz, r-release (x86_64): vanquish_1.0.0.tgz, r-oldrel (x86_64): vanquish_1.0.0.tgz


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