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

This functions prepares sequencing data sets for a MeDeCom run.

prepare_data_BS(RNB_SET, WORK_DIR = getwd(),
  analysis.name = "analysis", SAMPLE_SELECTION_COL = NA,
  SAMPLE_SELECTION_GREP = NA, REF_CT_COLUMN = NA, PHENO_COLUMNS = NA,
  PREPARE_TRUE_PROPORTIONS = FALSE, TRUE_A_TOKEN = NA,
  HOUSEMAN_A_TOKEN = NA,
  ID_COLUMN = rnb.getOption("identifiers.column"),
  FILTER_COVERAGE = hasCovg(RNB_SET), MIN_COVERAGE = 5,
  MIN_COVG_QUANT = 0.05, MAX_COVG_QUANT = 0.95, FILTER_NA = TRUE,
  FILTER_SNP = TRUE, snp.list = NULL, FILTER_SOMATIC = TRUE)

`RNB_SET`	An object of type `RnBiseqSet-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`.
`REF_CT_COLUMN`	Column name in `RNB_SET` used to extract methylation information on the reference cell types.
`PHENO_COLUMNS`	Vector of column names in the phenotypic table of `RNB_SET` that is kept and exported for further exploration.
`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.
`ID_COLUMN`	Sample-specific ID column name in `RNB_SET`
`FILTER_COVERAGE`	Flag indicating, if site-filtering based on coverage is to be conducted.
`MIN_COVERAGE`	Minimum number of reads required in each sample for the site to be considered for adding to MeDeCom.
`MIN_COVG_QUANT`	Lower quantile of coverages. Values lower than this value will be ignored for analysis.
`MAX_COVG_QUANT`	Upper quantile of coverages. Values higher than this value will be ignored for analysis.
`FILTER_NA`	Flag indicating if sites with any missing values are to be removed or not.
`FILTER_SNP`	Flag indicating if annotated SNPs are to be removed from the list of sites according to RnBeads' SNP list.
`snp.list`	Path to a file containing positions of known SNPs to be removed from the analysis, if `FILTER_SNP` is `TRUE`. The coordinates must be the provided in the same genome assembly as RNB_SET. The file must be a tab-separated value (tsv) file with only one header line an the following meaning of the rows: 1st row: chromosome, 2nd row: position of the SNP on the chromosome
`FILTER_SOMATIC`	Flag indicating if only somatic probes are to be kept.