GetVAF: Extract the VAFs (variant allele frequencies) and read depth...
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description Usage Arguments Value Examples

Extract the VAFs (variant allele frequencies) and read depth information from a VCF file

GetStrelkaVAF(vcf, name.of.VCF = NULL)

GetMutectVAF(vcf, name.of.VCF = NULL, tumor.col.name = NA)

GetFreebayesVAF(vcf, name.of.VCF = NULL)

`vcf`	Said VCF as a data.frame.
`name.of.VCF`	Name of the VCF file.
`tumor.col.name`	Optional. Only applicable to Mutect VCF. Name of the column in Mutect 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.

The original vcf with two additional columns added which contain the VAF(variant allele frequency) and read depth information.

file <- c(system.file("extdata/Strelka-SBS-vcf",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
MakeDataFrameFromVCF <- getFromNamespace("MakeDataFrameFromVCF", "ICAMS")
df <- MakeDataFrameFromVCF(file)
df1 <- GetStrelkaVAF(df)