exportDB.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eRNAkitDB.R
\name{exportDB}
\alias{exportDB}
\title{Write eRNAkit Database to Standard Bioinformatics File}
\usage{
exportDB(
  db = eRNAkitDB,
  output = "eRNADBv0.2.2.gtf",
  format = "gtf",
  chr = F,
  mito = NULL
)
}
\arguments{
\item{db}{A list representing the eRNAkit database object. Must contain
\code{core} data.frame with columns \code{chr}, \code{start}, and \code{end},
and \code{E_sequence} data.frame with \code{label} and \code{sequence} columns.
Defaults to \code{eRNAkitDB}.}

\item{output}{Character string specifying the output file path or name.
Defaults to \code{"eRNADBv0.2.2.gtf"}.}

\item{format}{Character string indicating the output format, one of
\code{"bed"}, \code{"gtf"}, or \code{"fasta"}. Default is \code{"gtf"}.}

\item{chr}{Logical; if \code{TRUE}, ensures chromosome names start with \code{"chr"},
otherwise removes \code{"chr"} prefix. Default is \code{FALSE}.}

\item{mito}{Optional character string to rename mitochondrial chromosome
labels (e.g., \code{"chrM"} to \code{"MT"}). Default is \code{NULL}.}
}
\value{
Invisibly returns \code{NULL}. Writes output to the specified file.
}
\description{
Export the core data in an eRNAkit database to a file in one of the
common bioinformatics formats: BED, GTF, or FASTA.
}
\details{
This function converts the core annotation and sequence data stored in the eRNAkit
database to a chosen file format, writing to disk with optional metadata appended
as header comments (for BED/GTF) or embedded in FASTA headers.
}
\examples{
\dontrun{
exportDB(db=eRNAkitDB, mito="MT") # For ensemble
exportDB(output="eRNADB_chrv0.2.2.gtf", chr=T, mito="MT") # for ensemble
exportDB(db=eRNAkitDB, output="eRNADBv0.2.2.bed", format="bed", mito="MT")
exportDB(db=eRNAkitDB, output="eRNADBv0.2.2.fa", format="fasta")
}

}