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 = 1,
      min.normals.betafit = 7,
      min.median.coverage.betafit = 5,
      yieldSize = 5000,
      genome
    )

### Arguments

`normal.panel.vcf.file` | `character(1)` Combined VCF file of a panel of normals, reference and alt counts as AD genotype field. Needs to be compressed and indexed with bgzip and tabix, respectively.
`min.normals` | Minimum number of normals with heterozygous SNP for calculating position-specific mapping bias.
`min.normals.betafit` | Minimum number of normals with heterozygous SNP fitting a beta distribution
`min.median.coverage.betafit` | Minimum median coverage of normals with heterozygous SNP for fitting a beta distribution
`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 1.22.2 Index]