library(FIREVAT)
# Sample VCF file
sample.vcf.file <- system.file("extdata", "DCC_PCAWG_Cell_Lines_HCC1954_GERMLINE.vcf", package = "FIREVAT")
# Config file
config.file <- system.file("config", "PCAWG_DKFZ_Cell_Line_Filtering_Params.json", package = "FIREVAT")
# Run FIREVAT
results <- RunFIREVAT(vcf.file = sample.vcf.file,
vcf.file.genome = 'hg19',
config.file = config.file,
mode = "manual",
df.ref.mut.sigs = GetPCAWGMutSigs(),
target.mut.sigs = GetPCAWGMutSigsNames(),
sequencing.artifact.mut.sigs = PCAWG.All.Sequencing.Artifact.Signatures,
output.dir = "",
num.cores = 1,
mutalisk.random.sampling.count = 20,
mutalisk.random.sampling.max.iter = 10,
annotate = FALSE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.