prepare_data: GLOBALS FUNCTIONS prepare_data
In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

This functions prepares Illumina BeadChip data for a MeDeCom run.

prepare_data(RNB_SET, WORK_DIR = getwd(), analysis.name = "analysis",
  SAMPLE_SELECTION_COL = NA, SAMPLE_SELECTION_GREP = NA,
  PHENO_COLUMNS = NA, ID_COLUMN = rnb.getOption("identifiers.column"),
  NORMALIZATION = "none", REF_CT_COLUMN = NA, REF_RNB_SET = NULL,
  REF_RNB_CT_COLUMN = NA, PREPARE_TRUE_PROPORTIONS = FALSE,
  TRUE_A_TOKEN = NA, HOUSEMAN_A_TOKEN = NA,
  ESTIMATE_HOUSEMAN_PROP = FALSE,
  FILTER_BEADS = !is.null(RNB_SET@covg.sites), MIN_N_BEADS = 3,
  FILTER_INTENSITY = inherits(RNB_SET, "RnBeadRawSet"),
  MIN_INT_QUANT = 0.01, MAX_INT_QUANT = 0.99, FILTER_NA = TRUE,
  FILTER_CONTEXT = TRUE, FILTER_SNP = TRUE, FILTER_SOMATIC = TRUE,
  FILTER_CROSS_REACTIVE = T, remove.ICA = F, conf.fact.ICA = NULL,
  ica.setting = NULL, snp.list = NULL, execute.lump = FALSE,
  dist.snps = FALSE)

`RNB_SET`	An object of type `RnBSet-class` for which analysis is to be performed.
`WORK_DIR`	A path to a existing directory, in which the results are to be stored
`analysis.name`	A string representing the dataset for which analysis is to be performed. Only used to create a folder with a descriptive name of the analysis.
`SAMPLE_SELECTION_COL`	A column name in the phenotypic table of `RNB_SET` used to selected a subset of samples for analysis that contain the string given in `SAMPLE_SELECTION_GREP`.
`SAMPLE_SELECTION_GREP`	A string used for selecting samples in the column `SAMPLE_SELECTION_COL`.
`PHENO_COLUMNS`	Vector of column names in the phenotypic table of `RNB_SET` that is kept and exported for further exploration.
`ID_COLUMN`	Sample-specific ID column name in `RNB_SET`
`NORMALIZATION`	Normalization method to be performed before employing MeDeCom. Can be one of `"none","dasen","illumina","noob"`.
`REF_CT_COLUMN`	Column name in `RNB_SET` used to extract methylation information on the reference cell types.
`REF_RNB_SET`	An object of type `RnBSet-class` containing methylation information on reference cell types.
`REF_RNB_CT_COLUMN`	Column name in `REF_RNB_SET` used to extract methylation information on the reference cell types.
`PREPARE_TRUE_PROPORTIONS`	Flag indicating if true proportions are either available in `RNB_SET` or to be estimated with Houseman's reference-based deconvolution approach.
`TRUE_A_TOKEN`	String present in the column names of `RNB_SET` used for selecting the true proportions of the corresponding cell types.
`HOUSEMAN_A_TOKEN`	Similar to `TRUE_A_TOKEN`, but not containing the true proportions, rather the estimated proportions by Houseman's method.
`ESTIMATE_HOUSEMAN_PROP`	If neither `TRUE_A_TOKEN` nor `HOUSEMAN_A_TOKEN` are given, the proportions of the reference cell type are estimated with Houseman's approach.
`FILTER_BEADS`	Flag indicating, if site-filtering based on the number of beads available is to be conducted.
`MIN_N_BEADS`	Minimum number of beads required in each sample for the site to be considered for adding to MeDeCom.
`FILTER_INTENSITY`	Flag indicating if sites should be removed according to the signal intensities (the lowest and highest quantiles given by `MIN_INT_QUANT` and `MAX_INT_QUANT`). Note that all sites are removed that have a value outside of the provided quantile range in either of the channels and in any of the samples.
`MIN_INT_QUANT`	Lower quantile of intensities which is to be removed.
`MAX_INT_QUANT`	Upper quantile of intensities which is to be removed.
`FILTER_NA`	Flag indicating if sites with any missing values are to be removed or not.
`FILTER_CONTEXT`	Flag indicating if only CG probes are to be kept.
`FILTER_SNP`	Flag indicating if annotated SNPs are to be removed from the list of sites according to RnBeads' SNP list. Or as the sites specified in `snp.list`.
`FILTER_SOMATIC`	Flag indicating if only somatic probes are to be kept.
`FILTER_CROSS_REACTIVE`	Flag indicating if sites showing cross reactivity on the array are to be removed.
`remove.ICA`	Flag indicating if independent component analysis is to be executed to remove potential confounding factor. If `TRUE`,conf.fact.ICA needs to be specified.
`conf.fact.ICA`	A vector of column names in the sample annotation sheet representing potential confounding factors.
`ica.setting`	Named vector of settings passed to run.rnb.ica. Options are `nmin, nmax, thres.sd, alpha.fact, save.report, alpha.feat, type, ncores`. See `run.rnb.ica` for further details. NULL indicates the default setting.
`snp.list`	Path to a file containing CpG IDs of known SNPs to be removed from the analysis, if `FILTER_SNP` is `TRUE`.
`execute.lump`	Flag indicating if the LUMP algorithm is to be used for estimating the amount of immune cells in a particular sample.
`dist.snps`	Flag indicating if SNPs are to removed by determining if the pairwise differences between the CpGs in the samples are trimodally distributed as it is frequently found around SNPs.