rmChangePoint

threshold

skew

Lower bound for allele frequency region

lower

Upper bound for allele frequency region

upper

Remove CNV regions within VCF files by changepoint method

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.

rmChangePoint: Remove CNV regions within VCF files by changepoint method

Description

Usage

Arguments

Value