auxProcessVariants: auxProcessVariants

View source: R/loadVCFs.R

auxProcessVariantsR Documentation

auxProcessVariants

Description

Auxiliar function called by loadVCFs to process variants

Usage

auxProcessVariants(
  vars,
  cnvGR,
  heterozygous.range,
  homozygous.range,
  min.total.depth,
  exclude.indels,
  regions.to.exclude
)

Arguments

vars

GRanges object containing variants for a certain sample.

cnvGR

GRanges object containg CNV calls for a certain sample.

heterozygous.range

Heterozygous range. Variants not in the homozygous/heterozygous intervals will be excluded.

homozygous.range

Homozygous range. Variants not in the homozygous/heterozygous intervals will be excluded.

min.total.depth

Minimum total depth. Variants under this value will be excluded.

exclude.indels

Whether to exclude indels when loading the variants. TRUE is the recommended value given that indels frequency varies in a different way than SNVs.

regions.to.exclude

A GRanges object defining the regions for which the variants should be excluded.

Value

Processed vars


jpuntomarcos/CNVfilteR documentation built on Oct. 6, 2023, 12:37 a.m.