sssc: Same Species Sample Contamination Detection

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.

Getting started

Package details

AuthorTao Jiang [aut, cre]
MaintainerTao Jiang <>
Package repositoryView on CRAN
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sssc documentation built on May 2, 2019, 4:03 p.m.