| 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