calculateMappingBiasVcf {PureCN}R Documentation

Calculate Mapping Bias

Description

Function calculate mapping bias for each variant in the provided panel of normals VCF.

Usage

calculateMappingBiasVcf(normal.panel.vcf.file, min.normals = 2,
  yieldSize = 5000, genome)

Arguments

normal.panel.vcf.file

Combined VCF file of a panel of normals, reference and alt counts as AD genotype field. Should be compressed and indexed with bgzip and tabix, respectively.

min.normals

Minimum number of normals with heterozygous SNP for calculating position-specific mapping bias. Requires normal.panel.vcf.file.

yieldSize

See TabixFile

genome

See readVcf

Value

A GRanges object with mapping bias and number of normal samples with this variant.

Author(s)

Markus Riester

Examples


normal.panel.vcf <- system.file("extdata", "normalpanel.vcf.gz", package="PureCN")
bias <- calculateMappingBiasVcf(normal.panel.vcf, genome = "h19")
saveRDS(bias, "mapping_bias.rds")


[Package PureCN version 1.14.1 Index]