calculateMappingBiasVcf: Calculate Mapping Bias

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

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.normals.assign.betafit = 3,
  min.normals.position.specific.fit = 10,
  min.median.coverage.betafit = 5,
  num.betafit.clusters = 9,
  min.betafit.rho = 1e-04,
  max.betafit.rho = 0.2,
  yieldSize = 50000,
  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 binomial distribution
min.normals.assign.betafit	Minimum number of normals with heterozygous SNPs to assign to a beta binomal fit cluster
min.normals.position.specific.fit	Minimum normals to use position-specific beta-binomial fits. Otherwise only clustered fits are used.
min.median.coverage.betafit	Minimum median coverage of normals with heterozygous SNP for fitting a beta binomial distribution
num.betafit.clusters	Maximum number of beta binomial fit clusters
min.betafit.rho	Minimum dispersion factor rho
max.betafit.rho	Maximum dispersion factor rho
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")

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