ICAMS (version 2.0.7)

GetVAF: Extract the VAFs (variant allele frequencies) from a VCF file.

Description

Extract the VAFs (variant allele frequencies) from a VCF file.

Usage

GetStrelkaVAF(vcf)

GetMutectVAF(vcf)

Arguments

vcf

Said VCF as a data.frame.

Value

A vector of VAFs, one for each row of vcf.

Examples

Run this code
# NOT RUN {
file <- c(system.file("extdata",
                      "Strelka.SBS.GRCh37.vcf",
                      package = "ICAMS"))
MakeDataFrameFromStrelkaSBSVCF <- 
  getFromNamespace("MakeDataFrameFromStrelkaSBSVCF", "ICAMS")
df <- MakeDataFrameFromStrelkaSBSVCF(file)
vaf <- GetStrelkaVAF(df)
# }

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