% 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")

}