ICAMS (version 2.0.10)

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, name.of.VCF = NULL, tumor.col.name = NA)

Arguments

vcf

Said VCF as a data.frame.

name.of.VCF

Name of the VCF file.

tumor.col.name

Name of the column in VCF which contains the tumor sample information. It must have quotation marks. If tumor.col.name is equal to NA(default), this function will use the 10th column to calculate VAFs.

Value

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

Examples

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