data-raw/old.code.and.notes/example.scripts/z4K25b10000n2000.R

In steverozen/mSigHdp: Mutational signature discovery using HDP (hierarchical Dirichlet process)

# Example script for running RunAndEvalHdp5 or RunAndEvalHdp4

library(mSigHdp)

prog.number <- 4
if (prog.number == 4) {
  my.fn    <- RunAndEvalHdp4
} else if (prog.number == 5) {
  my.fn <- RunAndEvalHdp5
}

root.dir <- "."
seed     <- 7744
num.jobs <- 10
burnin   <- 10000
K.guess  <- 25
n        <- 2000

out.dir  <-
  file.path(root.dir,
            paste("z.out.dir",
                  "seed", seed,
                  "burnin", burnin,
                  "K", K.guess,
                  "n", n,
                  "prog", prog.number, sep = "."))
dir.create(out.dir, recursive = TRUE)
of <- file(file.path(out.dir, "out.txt"), open = "wt")
sink(file = of, type = "output")
ef <- file(file.path(out.dir, "err.txt"), open = "wt")
sink(file = ef, type = "message")
my.fn

system.time(
  retval <- my.fn(
    input.catalog       = file.path(root.dir, "ground.truth.syn.catalog.csv"),
    ground.truth.exposure.file = file.path(root.dir,
                                           "ground.truth.syn.exposures.csv"),
    ground.truth.sig.file      = file.path(root.dir,
                                           "ground.truth.syn.sigs.csv"),
    out.dir                    = out.dir,
    CPU.cores          = num.jobs,
    seedNumber         = seed,
    K.guess            = K.guess,
    post.burnin        = burnin,
    post.n             = n,
    post.space         = 10,
    multi.types        = FALSE,
    overwrite          = TRUE,
    num.posterior      = num.jobs))

# nice R --vanilla < z4K25b10000n2000.R > out.z4K25b10000n2000.txt &> err.z4K25.b10000n2000.txt &