defcon: DEtection of Frequency CONtamination

In vanquish: Variant Quality Investigation Helper

Description

Detects whether a sample is contaminated another sample of its same species. The input file should be in vcf format.

Usage

defcon(file, rmCNV = FALSE, cnvobj = NULL, config = NULL,
  class_model = NULL, regression_model = NULL)

Arguments

file	VCF input object
rmCNV	Remove CNV regions, default is FALSE
cnvobj	CNV object, default is NULL
config	config information of parameters. A default set is generated as part of the model and is included in a model object, which contains
class_model	An SVM classification model
regression_model	An SVM regression model

Value

A list containing (1) stat: a data frame with all statistics for contamination estimation; (2) result: contamination estimation (Class = 0, pure; Class = 1, contaminated)

Examples

data(vcf_example)
result <- defcon(file = vcf_example)

vanquish documentation built on May 2, 2019, 9:42 a.m.