create_anno_region: Create annotation regions
In andreaskapou/BPRMeth: Model higher-order methylation profiles

Description Usage Arguments Value Author(s) See Also Examples

create_anno_region creates annotation regions from annotation data, using the central point of the annotation features as ground truth labels we create genomic regions N bp upstream and M bp downstream of central location.

create_anno_region(
  anno,
  chrom_size = NULL,
  is_centre = FALSE,
  is_window = TRUE,
  upstream = -5000,
  downstream = 5000
)

`anno`	A `GRanges` object containing the annotation data, this normally would be the output from `read_anno` function.
`chrom_size`	Object containing genome chromosome sizes, normally would be the output of `read_chrom_size` function.
`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.

A GRanges object containing the genomic regions.

The GRanges object contains two or three additional metadata column:

id: Genomic region id.
centre: Central location of each genomic region.
name: (Optional) Genomic region name.

This column can be accessed as follows: granges_object$tss

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

create_region_object, read_anno

# Obtain the path to files
file <- system.file("extdata", "dummy_anno.bed", package = "BPRMeth")
anno_dt <- read_anno(file, is_anno_region = FALSE)
# Create genomic region
gen_region <- create_anno_region(anno_dt)
# Extract ID
id <- gen_region$id