RunhdpLessHier: Run hdp extraction and attribution on a spectra catalog file

In WuyangFF95/SynSigRun: Run Mutational Signature Analysis Software Packages Using Mutational Spectra generated by SynSigGen

Run hdp extraction and attribution on a spectra catalog file

Description

Run hdp extraction and attribution on a spectra catalog file

Usage

RunhdpLessHier(
  input.catalog,
  out.dir,
  CPU.cores = 1,
  seedNumber = 1,
  K.guess,
  multi.types = FALSE,
  remove.noise = FALSE,
  num.posterior = 4,
  post.burnin = 4000,
  post.n = 50,
  post.space = 50,
  post.cpiter = 3,
  test.only = FALSE,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

input.catalog	File containing a spectra catalog in ICAMS format.
out.dir	Directory that will be created for the output; abort if it already exits. Log files will be in paste0(out.dir, "/tmp").
CPU.cores	Number of CPUs to use in running hdp_posterior.
seedNumber	Specify the pseudo-random seed number used to run hdp. Setting seed can make the attribution of hdp repeatable. Default: 1.
K.guess	Suggested initial value of the number of signatures, passed to dp_activate as initcc.
multi.types	A logical scalar or a character vector. If FALSE, hdp will regard all input spectra as one tumor type, and will allocate them to one single dirichlet process node. If TRUE, hdp will infer tumor types based on the string before "::" in their names. e.g. Tumor type for "SA.Syn.Ovary-AdenoCA::S.500" would be "SA.Syn.Ovary-AdenoCA" If it is a character vector, it should be a vector of case-sensitive tumor types. e.g. c("SA.Syn.Ovary-AdenoCA", "SA.Syn.Ovary-AdenoCA", "SA.Syn.Kidney-RCC").
remove.noise	Whether to remove noise signature "hdp.0"? In normal cases scenarios, only few mutations will be assigned to noise signature. For result visualization and assessment of hdp package, select TRUE; for diagnostic purposes, select FALSE.
num.posterior	Number of posterior sampling chains; can set to 1 for testing.
post.burnin	Pass to hdp_posterior burnin.
post.n	Pass to hdp_posterior n.
post.space	Pass to hdp_posterior space.
post.cpiter	Pass to hdp_posterior cpiter.
test.only	If TRUE, only analyze the first 10 columns in input.catalog.
overwrite	If TRUE, overwrite existing output.
verbose	If TRUE then message progress information.

Details

Creates several files in out.dir. These are: TODO(Steve): list the files

TODO(Wuyang)

Value

The inferred exposure of hdp, invisibly.

WuyangFF95/SynSigRun documentation built on Oct. 7, 2022, 1:16 p.m.