PureCN (version 1.0.3)

setPriorVcf: 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, 0.95, 0.01), verbose = TRUE)

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 dbSNP (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 > 2 to the first of those values in case of no matched normal available (0.95 default). Final value is for the case that variant is in both dbSNP and COSMIC > 2.
verbose
Verbose output.

Value

  • A vector with the prior probability of somatic status for each variant in the CollapsedVCF.

Examples

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

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