run_batcave: Run the BATCAVE algorithm
In bmannakee/batcaver:

Description Usage Arguments Value

View source: R/batcaver.R

Run the BATCAVE algorithm

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run_batcave(vcf, reference, file_type = "vcf", seq_type = "wgs",
  sample_name = "TUMOR", min_vaf = 0.05, min_odds = 10,
  plot_path = NULL, profile_path = NULL)

`vcf`	Output of MuTect 1.1.7 (call stats) or 2.0 (VCF 4.0).
`reference`	The genome reference used for alignment and variant calling (BSgenome Object)
`file_type`	The file type of "vcf" (default = "vcf")
`seq_type`	The type of sequencing experiment. Whole Genome "wgs" or Whole Exome "wes" (default = "wgs")
`sample_name`	The name of the tumor sample (default = "TUMOR")
`min_vaf`	The minimum allele frequency to use to compute mutation rate per base (default = "0.05)
`min_odds`	The odds ratio cutoff for high-confidence mutations used to compute prior probability of mutation (default = "10" which corresponds to MuTect TLOD = 7.3)
`plot_path`	The file name to use for a plot of the empirical mutation profile (default = "NULL" for no plot)
`profile_path`	The file name to use for a tab separated file containing the empirical mutation profile (default = "NULL" for no file)

a data frame with 11 columns: chrom the chromosome the variant is on, start and end the position of the variant, ref and alt the reference and alternate alleles, context the tri-nucleotide context of the variant, TLOD the score reported by MuTect, freq the variant allele frequency, pass_all a boolean column that is TRUE is the variant passed all MuTect filters and FALSE otherwise, tlod_only a boolean column that is TRUE is the variant passed all MuTect filters except the TLOD filter and false otherwise, pprob_variant the posterior probability for the variant computed using the BATCAVE algorithm

@examples ## Not run: ## input files and varianbles library(BSgenome.Hsapiens.UCSC.hg38) # the BSgenome reference vcf <- /path/to/MuTect/vcf reference <- BSgenome.Hsapiens.UCSC.hg38 file_type <- "vcf" seq_type <- "wes" sample_name <- "TUMOR" min_vaf <- .1 min_odds <- 10 plot_path <- /path/to/empirical/profile/plot.pdf profile_path <- /path/to/empirical/profile/profile.tsv fr <- run_batcave(vcf = vcf, reference = reference, file_type = file_type, seq_type = seq_type, sample_name = sample_name, min_vaf = min_vaf, min_odds = min_odds, plot_path = plot_path, profile_path = profile_path) ## End(Not run)

bmannakee/batcaver documentation built on Jan. 6, 2020, 5:29 a.m.