setMappingBiasVcf {PureCN} | R Documentation

## Set Mapping Bias VCF

### Description

Function to set mapping bias for each variant in the provided `CollapsedVCF` object. By default, it returns the same value for all variants, but a pool of normal samples can be provided for position-specific mapping bias calculation.

### Usage

    setMappingBiasVcf(vcf, tumor.id.in.vcf = NULL, normal.panel.vcf.file = NULL,
      min.normals = 2, smooth = TRUE, smooth.n = 5)

### Arguments

`vcf` | `CollapsedVCF` object, read in with the `readVcf` function from the VariantAnnotation package.
`tumor.id.in.vcf` | Id of tumor in case multiple samples are stored in VCF.
`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. One can provide a precomputed mapping bias database (obtained by `calculateMappingBiasVcf`).
`min.normals` | Minimum number of normals with heterozygous SNP for calculating position-specific mapping bias. Requires `normal.panel.vcf.file`.
`smooth` | Impute mapping bias of variants not found in the panel by smoothing of neighboring SNPs. Requires `normal.panel.vcf.file`.
`smooth.n` | Number of neighboring variants used for smoothing.

### Value

A list with elements

`bias` | A `numeric(nrow(vcf))` vector with the mapping bias of for each variant in the `CollapsedVCF`. Mapping bias is expected as scaling factor. Adjusted allelic fraction is (observed allelic fraction)/(mapping bias). Maximum scaling factor is 1 and means no bias.
`pon.count` | A `numeric(nrow(vcf))` vector with the number of hits in the `normal.panel.vcf.file`.

### Author(s)

Markus Riester

### Examples

    # This function is typically only called by runAbsoluteCN via
    # fun.setMappingBiasVcf and args.setMappingBiasVcf.
    vcf.file <- system.file("extdata", "example.vcf.gz", package="PureCN")
    vcf <- readVcf(vcf.file, "hg19")
    vcf.bias <- setMappingBiasVcf(vcf)

[Package PureCN version 1.12.2 Index]