create_prom_region: Create promoter regions from gene annotation data.
In andreaskapou/BPRMeth-devel: Model higher-order methylation profiles

Description Usage Arguments Value Author(s) See Also Examples

create_prom_region creates promoter region from gene annotation data. Using the TSS of gene annotation data as ground truth labels we create promoter regions N bp upstream and M bp downstream of TSS.

1 2	create_prom_region(annot_data, chrom_size = NULL, upstream = -7000, downstream = 7000)

`annot_data`	A `GRanges` object containing the gene annotation data. This for example can be RNA-Seq data output from `read_rna_encode_caltech`.
`chrom_size`	Optional `data.table` containing chromosome sizes, e.g. using the `read_chrom_size` function.
`upstream`	Integer defining the length of bp upstream of TSS.
`downstream`	Integer defining the length of bp downstream of TSS.

A GRanges object containing the promoter regions data.

The GRanges object contains one additional metadata column:

tss: TSS of each gene promoter.

This column can be accessed as follows: granges_object$tss

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

create_methyl_region, read_chrom_size, read_rna_encode_caltech

# Obtain the path to the file and then read it
rnaseq_file <- system.file("extdata", "rnaseq.bed", package = "BPRMeth")
annot_data <- read_rna_encode_caltech(rnaseq_file)
prom_region <- create_prom_region(annot_data)

# Extract the TSS
tss <- prom_region$tss