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 <[email protected]>
LicenseGPL-2
Version1.0.0
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("sssc")

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sssc documentation built on June 16, 2018, 1:39 p.m.