% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/bipartites.R
\name{bipartite_peaks2genes}
\alias{bipartite_peaks2genes}
\title{Compute links between DNA regions and genenames}
\usage{
bipartite_peaks2genes(
  hummus_object,
  gene_assay = "RNA",
  peak_assay = "peaks",
  gene_multiplex_name = NULL,
  peak_multiplex_name = NULL,
  peak_to_gene_method = "Signac",
  upstream = 500,
  downstream = 500,
  only_tss = TRUE,
  store_network = FALSE,
  output_file = NULL,
  bipartite_name = "atac_rna"
)
}
\arguments{
\item{hummus_object}{(hummus_object) - Hummus object.}

\item{gene_assay}{(character) - Name of assay containing the gene expression
data. Default: "RNA".}

\item{peak_assay}{(character) - Name of the assay containing the DNA regions
(ATAC peaks). Default: "peaks".}

\item{gene_multiplex_name}{(character) - Name of the multiplex containing the
genes.
If NULL, the name of the gene assay is used.}

\item{peak_multiplex_name}{(character) - Name of the multiplex containing the
DNA regions (ATAC peaks). If NULL, the name of the peak assay is used.}

\item{peak_to_gene_method}{(character) - Method to use to compute the links
between peaks and genes. 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{only_tss}{(logical) - If TRUE, only TSS will be considered.}

\item{store_network}{(bool) - Save the bipartite directly
(\code{TRUE}, default) or return without saving on disk (\code{FALSE}).}

\item{output_file}{(character) - Name of the output_file
(if store_bipartite == \code{TRUE}). Default: NULL.}

\item{bipartite_name}{(character) - Name of bipartite. Default: "atac_rna".}

\item{verbose}{(integer) Display function messages.
Set to 0 for no message displayed, >= 1 for more details. Default: 1.}
}
\value{
hummus_object (hummus_object) - Hummus object w/ atac-rna bipartite
added to the multilayer slot
}
\description{
Compute and add bipartite between DNA regions and genenames to hummus object.
Links are computed based on the distance between peaks and gene's TSS
location from gene.range annotations.
Call find_peaks_near_genes function, that can use different methods.
}
\examples{
hummus <- bipartite_peaks2genes(
                       hummus_object = hummus,
                       gene_assay = "RNA",
                       peak_assay = "peaks",
                       gene_multiplex_name = "RNA",
                       peak_multiplex_name = "peaks",
                       peak_to_gene_method = "Signac",
                       upstream = 500,
                       downstream = 500,
                       only_tss = TRUE,
                       store_network = FALSE,
                       bipartite_name = "atac_rna")
}