granges_overlap.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/granges_overlap.R
\name{granges_overlap}
\alias{granges_overlap}
\title{Find GenomicRanges overlap
 
Find overlap genomic position overlap between two
\link[GenomicRanges]{GRanges} objects.}
\usage{
granges_overlap(
  dat1,
  dat2,
  chrom_col.1 = "chrom",
  start_col.1 = "start",
  end_col.1 = start_col.1,
  chrom_col.2 = "chrom",
  start_col.2 = "start",
  end_col.2 = end_col.2,
  return_merged = TRUE,
  unique_only = TRUE,
  style = "NCBI",
  verbose = FALSE
)
}
\arguments{
\item{dat1}{Dataset 1 
(can be \link[GenomicRanges]{GRanges} or \link[data.table]{data.table}).}

\item{dat2}{Dataset 2.
(can be \link[GenomicRanges]{GRanges} or \link[data.table]{data.table}).}

\item{chrom_col.1}{Name of the chromosome column in \code{dat1}.}

\item{start_col.1}{Name of the start position column in \code{dat1}.}

\item{end_col.1}{Name of the end position column in \code{dat2}.}

\item{chrom_col.2}{Name of the chromosome column in \code{dat2}.}

\item{start_col.2}{Name of the start position column in \code{dat2}.}

\item{end_col.2}{Name of the end position column in \code{dat2}.}

\item{return_merged}{Whether to return an object with columns
from \code{dat1} and \code{dat2} merged.}

\item{unique_only}{Only return unique rows.}

\item{style}{GRanges style (e.g. "NCBI, "UCSC") 
set by \link[GenomeInfoDb]{seqlevelsStyle}.}

\item{verbose}{Print messages.}
}
\description{
Find GenomicRanges overlap
 
Find overlap genomic position overlap between two
\link[GenomicRanges]{GRanges} objects.
}
\examples{
dat1 <- echodata::BST1
dat2 <- echoannot::xgr_example
GenomicRanges::mcols(dat2) <- NULL

gr.hits <- echoannot::granges_overlap(dat1 = dat1, 
                                      dat2 = dat2, 
                                      chrom_col.1 = "CHR",
                                      start_col.1 = "POS")
}
\concept{GRanges}