generate_feature {vanquish}R Documentation

Feature Generation for Contamination Detection Model

Description

Generates features from each pair of input VCF objects for training contamination detection model.

Usage

generate_feature(file, hom_p = 0.999, het_p = 0.5, hom_rho = 0.005,
  het_rho = 0.1, mixture, homcut = 0.99, highcut = 0.7, hetcut = 0.3)

Arguments

file

VCF input object

hom_p

The initial value for p in Homozygous Beta-Binomial model, default is 0.999

het_p

The initial value for p in Heterozygous Beta-Binomial model, default is 0.5

hom_rho

The initial value for rho in Homozygous Beta-Binomial model, default is 0.005

het_rho

The initial value for rho in Heterozygous Beta-Binomial model, default is 0.1

mixture

A vector of whether the sample is contaminated: 0 for pure; 1 for contaminated

homcut

Cutoff allele frequency value between hom and high, default is 0.99

highcut

Cutoff allele frequency value between high and het, default is 0.7

hetcut

Cutoff allele frequency value between het and low, default is 0.3

Value

A data frame with all features for training model of contamination detection


[Package vanquish version 1.0.0 Index]