start_medecom_analysis: start_medecom_analysis
In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

Wrapper for runMeDeCom, for data preprocessed through the DecompPipeline

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_RDIR = NA, CLUSTER_HOSTLIST = "*",
  CLUSTER_MEMLIMIT = "5G", CLEANUP = FALSE, analysis_info = NULL,
  LAMBDA_GRID_TYPE = "standard", ANALYSIS_TOKEN = "customAnalysis")

`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_RDIR`	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.