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vanquish
View on CRAN: Click
here
Download and install vanquish package within the R console
Install from CRAN:
install.packages("vanquish")
Install from Github:
library("remotes")
install_github("cran/vanquish")
Install by package version:
library("remotes")
install_version("vanquish", "1.0.0")
Attach the package and use:
library("vanquish")
Maintained by
Tao Jiang
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-09-05
Latest Update: 2018-09-05
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). vanquish: Variant Quality Investigation Helper. R package version 1.0.0, https://cran.r-project.org/web/packages/vanquish
Previous versions and publish date:
No previous versions
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Other R packages that vanquish depends,
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Functions, R codes and Examples using
the vanquish R package
Some associated functions: config_df . defcon . generate_feature . getAlt2 . getAnnoRate . getAvgLL . getLowDepth . getRatio . getSNVRate . getSkewness . getVar . locateFile . negll . readGATK . readStrelka . readVarDict . readVarPROWL . read_vcf . rho_est . rmCNVinVCF . rmChangePoint . summary_vcf . svm_class_model . svm_regression_model . train_ct . update_vcf . vcf_example .
Some associated R codes: data.R . defcon.R . generate_feature.R . read_vcf.R . rho_est.R . summary_vcf.R . train_ct.R . update_vcf.R . Full vanquish package functions and examples
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