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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 |
| DOI: | 10.32614/CRAN.package.vanquish |
| Author: | Tao Jiang [aut, cre] |
| Maintainer: | Tao Jiang <tjiang8 at ncsu.edu> |
| 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: vanquish_1.0.0.zip, r-release: vanquish_1.0.0.zip, r-oldrel: vanquish_1.0.0.zip |
| 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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