create_melissa_data_obj: Create methylation regions for all cells
In Melissa: Bayesian clustering and imputationa of single cell methylomes

Description Usage Arguments Value Author(s) See Also Examples

Wrapper function for creating methylation regions for all cells, which is the input object for Melissa prior to filtering.

create_melissa_data_obj(
  met_dir,
  anno_file,
  chrom_size_file = NULL,
  chr_discarded = NULL,
  is_centre = FALSE,
  is_window = TRUE,
  upstream = -5000,
  downstream = 5000,
  cov = 5,
  sd_thresh = -1,
  no_cores = NULL
)

`met_dir`	Directory of (binarised) methylation files, each file corresponds to a single cell.
`anno_file`	The annotation file with 'tab' delimited format: "chromosome", "start", "end", "strand", "id", "name" (optional). Read the 'BPRMeth' documentation for more details.
`chrom_size_file`	Optional file name to read genome chromosome sizes.
`chr_discarded`	Optional vector with chromosomes to be discarded.
`is_centre`	Logical, whether 'start' and 'end' locations are pre-centred. If TRUE, the mean of the locations will be chosen as centre. If FALSE, the 'start' will be chosen as the center; e.g. for genes the 'start' denotes the TSS and we use this as centre to obtain K-bp upstream and downstream of TSS.
`is_window`	Whether to consider a predefined window region around centre. If TRUE, then 'upstream' and 'downstream' parameters are used, otherwise we consider the whole region from start to end location.
`upstream`	Integer defining the length of bp upstream of 'centre' for creating the genomic region. If is_window = FALSE, this parameter is ignored.
`downstream`	Integer defining the length of bp downstream of 'centre' for creating the genomic region. If is_window = FALSE, this parameter is ignored.
`cov`	Integer defining the minimum coverage of CpGs that each region must contain.
`sd_thresh`	Optional numeric defining the minimum standard deviation of the methylation change in a region. This is used to filter regions with no methylation variability.
`no_cores`	Number of cores to be used for parallel processing of data.

A melissa_data_obj object, with the following elements:

met: A list of elements of length N, where N are the total number of cells. Each element in the list contains another list of length M, where M is the total number of genomic regions, e.g. promoters. Each element in the inner list is an I X 2 matrix, where I are the total number of observations. The first column contains the input observations x (i.e. CpG locations) and the 2nd column contains the corresponding methylation level.
anno_region: The annotation object.
opts: A list with the parameters that were used for creating the object.

C.A.Kapourani C.A.Kapourani@ed.ac.uk

binarise_files, melissa, filter_regions

## Not run: 
# Met directory
met_dir <- "name_of_met_dir"
# Annotation file name
anno_file <- "name_of_anno_file"

obj <- create_melissa_data_obj(met_dir, anno_file)

# Extract annotation regions
met <- obj$met

# Extract annotation regions
anno <- obj$anno_region

## End(Not run)