setMappingBiasVcf: Set Mapping Bias VCF

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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 mapping bias file can be provided for position-specific mapping bias calculation.

Usage

setMappingBiasVcf(
  vcf,
  tumor.id.in.vcf = NULL,
  mapping.bias.file = NULL,
  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.
mapping.bias.file	A precomputed mapping bias database obtained by calculateMappingBiasVcf. instead. reference and alt counts as AD genotype field. Should be compressed and
smooth	Impute mapping bias of variants not found in the panel by smoothing of neighboring SNPs. Requires mapping.bias.file.
smooth.n	Number of neighboring variants used for smoothing.

Value

Adds elements to the vcf INFO field

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 mapping.bias.file.
shape1, shape2	Fit of a beta distribution.

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)        

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.