start.medecom.analysis: start.medecom.analysis
In CompEpigen/DecompPipeline: Preparation pipeline for MeDeCom

View source: R/start_analysis.R

start.medecom.analysis

R Documentation

start.medecom.analysis

Description

Wrapper for runMeDeCom, for data preprocessed through the DecompPipeline

Usage

start.medecom.analysis(
  meth.data = NULL,
  rnb.set = NULL,
  work.dir = getwd(),
  cg.groups,
  Ks,
  lambda.grid,
  sample.subset = NULL,
  k.fixed = NULL,
  write.files = TRUE,
  factorviz.outputs = F,
  opt.method = "MeDeCom.cppTAfact",
  startT = NULL,
  startA = NULL,
  trueT = NULL,
  trueA = NULL,
  analysis.name = "MeDeComRun",
  folds = 10,
  cores = 1,
  itermax = 1000,
  ninit = 100,
  cluster.submit = FALSE,
  cluster.R.dir = NA,
  cluster.hostlist = "*",
  cluster.memlimit = "5G",
  cleanup = FALSE,
  analysis.info = NULL,
  lambda.grid.type = "standard",
  analysis.token = "customAnalysis"
)

Arguments

`meth.data`	A `matrix` or `data.frame` containing methylation information. If NULL, methylation information needs to be provided through `rnb.set`
`rnb.set`	An object of type `RnBSet-class` containing methylation and sample meta information.
`work.dir`	Working directory for the analysis.
`cg.groups`	List of CpG indices used for the analysis. Can be computed by `prepare.CG.subsets`.
`Ks`	Vector of integers used as components in MeDeCom.
`lambda.grid`	Vector of doubles representing the regularization parameter in MeDeCom.
`sample.subset`	Vector of indices of samples to be included in the analysis. If `NULL`, all samples are included.
`k.fixed`	Columns in the T matrix that should be fixed. If `NULL`, no columns are fixed.
`write.files`	Flag indicating if intermediate results are to be stored.
`factorviz.outputs`	Flag indicating, if outputs should be stored to be compatible with FactorViz for data exploration
`opt.method`	Optimization method to be used. Either MeDeCom.quadPen or MeDeCom.cppTAfact (default).
`startT`	Inital matrix for T.
`startA`	Initial matrix for A.
`trueT`	True value for the T matrix.
`trueA`	True value for the A matrix.
`analysis.name`	Name of the analysis.
`folds`	Integer representing the number of folds used in the analysis.
`cores`	Integer representing the number of cores to be used in the analysis.
`itermax`	Maximum number of iterations
`ninit`	Number if initialtions.
`cluster.submit`	Flag indicating, if the jobs are to be submitted to a scientific compute cluster (only SGE supported).
`cluster.R.dir`	Path to an executable version of R.
`cluster.hostlist`	Regular expression, on which basis hosts are selected in the cluster environment.
`cluster.memlimit`	the `memlimit` resource value of the cluster submission.
`cleanup`	Flag indicating if temprary files are to be deleted.
`analysis.info`	Information to be saved about the analysis. Just stored as info.
`lambda.grid.type`	String represent the lambda grid that was chosen. Just stored as info.
`analysis.token`	String specifying the type of analysis that was conducted. Just stored as info.