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sssc  

Same Species Sample Contamination Detection
View on CRAN: Click here


Download and install sssc package within the R console
Install from CRAN:
install.packages("sssc")

Install from Github:
library("remotes")
install_github("cran/sssc")

Install by package version:
library("remotes")
install_version("sssc", "1.0.0")



Attach the package and use:
library("sssc")
Maintained by
Tao Jiang
[Scholar Profile | Author Map]
First Published: 2018-06-15
Latest Update: 2018-06-15
Description:
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.
How to cite:
Tao Jiang (2018). sssc: Same Species Sample Contamination Detection. R package version 1.0.0, https://cran.r-project.org/web/packages/sssc. Accessed 29 Mar. 2025.
Previous versions and publish date:
No previous versions
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Complete documentation for sssc
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