% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/bipartites.R

\name{find_peaks_near_genes}

\alias{find_peaks_near_genes}

\title{Associate peaks to genes based on distance to TSS (or gene body)}

\usage{

find_peaks_near_genes(

  peaks,

  genes,

  sep = c("-", "-"),

  method = c("Signac", "GREAT"),

  upstream = 1e+05,

  downstream = 0,

  extend = 1e+06,

  only_tss = FALSE,

  verbose = TRUE

)

}

\arguments{

\item{peaks}{vector(character) - List of peaks.}

\item{genes}{vector(character) - List of genes.}

\item{sep}{vector(character) - Separator between chromosome,

start and end position. Default: c('-', '-').}

\item{method}{(character) - Method to use. Default: "Signac".

\itemize{

\item \code{'Signac'} - Use Signac::Extend to extend genes.

\item \code{'GREAT'} - Not implemented yet.

}}

\item{upstream}{(int) - Upstream distance from TSS

to consider as potential promoter.}

\item{downstream}{(int) - Downstream distance from TSS

to consider as potential promoter.}

\item{extend}{(int) - Integer defining the distance from the upstream

and downstream of the basal regulatory region. Used only by method 'GREAT'.}

\item{only_tss}{(logical) - If TRUE, only TSS will be considered.}

\item{verbose}{(logical) - If TRUE, print progress messages.}

}

\value{

(matrix) - Matrix of peaks x genes with 1 if peak is near gene.

}

\description{

Associate peaks to genes based on distance to TSS (or gene body)

}

\examples{

TODO

}