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 1.14.0 Index]