create_prom_region: Create promoter regions from gene annotation data.

In andreaskapou/processHTS: Process HTS Files and Data

Description

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.

Usage

create_prom_region(annot_data, chrom_size = NULL, upstream = -100,
  downstream = 100)

Arguments

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.

Value

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

Author(s)

C.A.Kapourani [e-mail]

See Also

create_methyl_region, read_chrom_size, read_rna_encode_caltech

Examples

# Load the annotation example dataset
ann_data <- annot_data
prom_regions <- create_prom_region(ann_data)

andreaskapou/processHTS documentation built on May 12, 2019, 3:33 a.m.