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.
Package details |
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Author | Tao Jiang [aut, cre] |
Maintainer | Tao Jiang <tjiang8@ncsu.edu> |
License | GPL-2 |
Version | 1.0.0 |
Package repository | View on CRAN |
Installation |
Install the latest version of this package by entering the following in R:
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