read_enh_beatson: Read Beatson bed formatted enhancer file
In andreaskapou/processHTS: Process HTS Files and Data

Description Usage Arguments Value Author(s) See Also Examples

read_enh_beatson reads a file containing enhancer annotation data using the fread function.

1 2	read_enh_beatson(enh_file, gene_file, chr_discarded = NULL, is_GRanges = TRUE)

`enh_file`	File containing enhancer annotation data
`gene_file`	File containing gene annotation data
`chr_discarded`	A vector with chromosome names to be discarded.
`is_GRanges`	Logical: if TRUE a GRanges object is returned, otherwise a data.frame object is returned.

A GRanges object if is_GRanges is TRUE, otherwise a data.table object.

The GRanges object contains three additional metadata columns:

ensembl_id: Ensembl IDs of each gene promoter.
gene_name: Gene name.

These columns can be accessed as follows: granges_object$ensembl_id

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

read_annot_beatson, read_bs_bismark_cov

# Get the location of the RNA-Seq file
enh_beatson_file <- system.file("extdata", "enhancers_beatson.bed", package = "processHTS")
rna_beatson_file <- system.file("extdata", "rna_beatson2.bed", package = "processHTS")

enh_beatson_data <- read_enh_beatson(enh_beatson_file, rna_beatson_file, chr_discarded = "chrX", is_GRanges=TRUE)