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 ncsu.edu>
License: GPL-2
NeedsCompilation: no
Materials: README
CRAN checks: vanquish results

Downloads:

Reference manual: vanquish.pdf
Package source: vanquish_1.0.0.tar.gz
Windows binaries: r-devel: vanquish_1.0.0.zip, r-release: vanquish_1.0.0.zip, r-oldrel: vanquish_1.0.0.zip
OS X binaries: r-release: vanquish_1.0.0.tgz, r-oldrel: vanquish_1.0.0.tgz

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