auxProcessVariants: auxProcessVariants

In jpuntomarcos/CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

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.