create_region_object: Create genomic region data
In andreaskapou/BPRMeth: Model higher-order methylation profiles

Description Usage Arguments Value Author(s) See Also Examples

create_region_object creates genomic regions (e.g. forms methylation regions data) using as input methylation and annotation data with genomic regions of interest.

create_region_object(
  met_dt,
  anno_dt,
  cov = 5,
  sd_thresh = 0.1,
  ignore_strand = TRUE,
  filter_empty_region = TRUE,
  fmin = -1,
  fmax = 1
)

`met_dt`	A `GRanges` object with methylation data, whose format should be similar to `read_met` function.
`anno_dt`	A `GRanges` object with annotation data, whose format should be similar to `read_anno`.
`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.
`ignore_strand`	Logical, whether or not to ignore strand information.
`filter_empty_region`	Logical, whether to discard genomic regions that have no CpG coverage or do not pass filtering options.
`fmin`	Minimum range value for location scaling. Under this version, it should be left to its default value -1.
`fmax`	Maximum range value for location scaling. Under this version, it should be left to its default value 1.

A list object containing the two elements:

met: A list containing methylation region data, where each entry in the list is an L_{i} X D dimensional matrix, where L_{i} denotes the number of CpGs found in region i. The columns contain the following information:
1. 1st column: Contains the locations of CpGs relative to centre. Note that the actual locations are scaled to the (fmin, fmax) region.
2. 2nd column: If "bulk" data (i.e. binomial) it contains the total number of reads at each CpG location, otherwise the methylation level.
3. 3rd column: If "bulk" data, the methylated reads at each CpG location, otherwise this D = 2 and this column is absent.
. Rownames of each matrix contain the actual CpG genomic coordinates as <chr>:<location>.
anno: The annotation object.

Note: The lengths of met and anno should match.

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

read_met, read_anno

## Not run: 
# Download the files and change the working directory to that location
met_dt <- read_met("name_of_met_file")
anno_dt <- read_anno("name_of_anno_file")

obj <- create_region_object(met_dt, anno_dt)

# Extract methylation regions
met <- obj$met

## End(Not run)