update_vcf

Remove CNV regions, default is FALSE

rmCNV

cnvobj

Threshold for allele frequency, default is 0.1

threshold

Skewness for allele frequency, default is 0.5

skew

Lower bound for allele frequency region, default is 0.45

lower

Upper bound for allele frequency region, default is 0.55

upper

Remove CNV regions within VCF files

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.

update_vcf: Remove CNV regions within VCF files

Description

Usage

Arguments

Value