defcon {vanquish}

DEtection of Frequency CONtamination

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)