setPriorVcf: Set Somatic Prior VCF

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

Set Somatic Prior VCF

Description

Function to set prior for somatic mutation status for each variant in the provided CollapsedVCF object.

Usage

setPriorVcf(
  vcf,
  prior.somatic = c(0.5, 5e-04, 0.999, 1e-04, 0.995, 0.5),
  tumor.id.in.vcf = NULL,
  min.cosmic.cnt = 6,
  DB.info.flag = "DB",
  Cosmic.CNT.info.field = "Cosmic.CNT"
)

Arguments

vcf	CollapsedVCF object, read in with the readVcf function from the VariantAnnotation package.
prior.somatic	Prior probabilities for somatic mutations. First value is for the case when no matched normals are available and the variant is not in germline databases (second value). Third value is for variants with MuTect somatic call. Different from 1, because somatic mutations in segments of copy number 0 have 0 probability and artifacts can thus have dramatic influence on likelihood score. Forth value is for variants not labeled as somatic by MuTect. Last two values are optional, if vcf contains a flag Cosmic.CNT, it will set the prior probability for variants with CNT > 6 to the first of those values in case of no matched normal available (0.995 default). Final value is for the case that variant is in both germline databases and COSMIC count > 6.
tumor.id.in.vcf	Id of tumor in case multiple samples are stored in VCF.
min.cosmic.cnt	Minimum number of hits in the COSMIC database to call variant as likely somatic.
DB.info.flag	Flag in INFO of VCF that marks presence in common germline databases. Defaults to DB that may contain somatic variants if it is from an unfiltered germline database.
Cosmic.CNT.info.field	Info field containing hits in the Cosmic database

Value

The vcf with numeric(nrow(vcf)) vector with the prior probability of somatic status for each variant in the CollapsedVCF added to the INFO field PR.

Author(s)

Markus Riester

Examples

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

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