setPriorVcf {PureCN} | R Documentation

## 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 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 (0.995 default). Final value is for the case that variant is in both dbSNP and COSMIC > 2.
`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 dbSNP VCF.
`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)

[Package PureCN version 2.0.2 Index]