Package: vanquish 1.0.0

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.

Authors:Tao Jiang [aut, cre]

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8 exports 0.00 score 34 dependencies 4 scripts 129 downloads

Last updated 6 years agofrom:7a9d817ba0. Checks:OK: 7. Indexed: yes.

Exports:defcongenerate_featuregetAlt2read_vcfrho_estsummary_vcftrain_ctupdate_vcf

Dependencies:changepointclassclicolorspacee1071fansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigproxyR6RColorBrewerrlangscalestibbleutf8vctrsVGAMviridisLitewithrzoo