% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/layers.R

\name{compute_tf_network}

\alias{compute_tf_network}

\title{Compute TF network and add it to hummus object}

\usage{

compute_tf_network(

  hummus,

  organism = 9606,

  tfs = NA,

  gene_assay = NULL,

  method = NULL,

  store_network = FALSE,

  output_file = NULL,

  source_target = "AND",

  multiplex_name = "TF",

  tf_network_name = "TF_network",

  verbose = 1

)

}

\arguments{

\item{hummus}{(Hummus_Object) - Hummus object}

\item{organism}{(integer)  - Specie identifier from Omnipath to fetch

specific interactions}

\item{tfs}{vector(character) - List of tfs consider. If NA, tfs are extracted

from the hummus object with get_tfs function.}

\item{gene_assay}{(character) - Name of the assay to get tfs from if tfs is

not provided. If NULL, all TFs with motifs in the hummus object are used.}

\item{method}{(character) - Method used to infer network edges.

\itemize{

\item \code{'Omnipath'} - Use Omnipath to infer tf-tf networks.

\item \code{'NULL'} - A fake connected network is computed.

\item \code{'Other method'} - TO DO.

}}

\item{store_network}{(bool) - Save the network directly (\code{TRUE},

default) or return without saving on disk (\code{FALSE}).}

\item{output_file}{(character) - Name of the output_file

(if store_network == \code{TRUE}).}

\item{source_target}{('AND'|'OR') - Fetch only the interactions involving

two considered tfs (\code{'AND', default}), or one considered tfs and any

other element (\code{'OR'})}

\item{multiplex_name}{(character) - Name of the multiplex to add the network

to. Default is \code{'TF'}.}

\item{tf_network_name}{(character) - Name of the network in the multiplex to

add the network to. Default is \code{'TF_network'}.}

\item{verbose}{(integer) - Display function messages. Set to 0 for no message

displayed, >= 1 for more details.}

}

\value{

(Hummus_Object) - Return hummus object with the new network added.

}

\description{

Compute a protein-protein interaction layer from Omnipath request that will represent tf cooperativity.

This network is the top-layer of HuMMuS multilayer.

}

\examples{

hummus <- compute_tf_network(hummus,

                                       gene_assay = "RNA",

                                       verbose = 1)

}