Extract the VAFs (variant allele frequencies) and read depth information from a VCF file
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
|
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.