|
a |
|
b/man/compute_tf_network.Rd |
|
|
1 |
% Generated by roxygen2: do not edit by hand |
|
|
2 |
% Please edit documentation in R/layers.R |
|
|
3 |
\name{compute_tf_network} |
|
|
4 |
\alias{compute_tf_network} |
|
|
5 |
\title{Compute TF network and add it to hummus object} |
|
|
6 |
\usage{ |
|
|
7 |
compute_tf_network( |
|
|
8 |
hummus, |
|
|
9 |
organism = 9606, |
|
|
10 |
tfs = NA, |
|
|
11 |
gene_assay = NULL, |
|
|
12 |
method = NULL, |
|
|
13 |
store_network = FALSE, |
|
|
14 |
output_file = NULL, |
|
|
15 |
source_target = "AND", |
|
|
16 |
multiplex_name = "TF", |
|
|
17 |
tf_network_name = "TF_network", |
|
|
18 |
verbose = 1 |
|
|
19 |
) |
|
|
20 |
} |
|
|
21 |
\arguments{ |
|
|
22 |
\item{hummus}{(Hummus_Object) - Hummus object} |
|
|
23 |
|
|
|
24 |
\item{organism}{(integer) - Specie identifier from Omnipath to fetch |
|
|
25 |
specific interactions} |
|
|
26 |
|
|
|
27 |
\item{tfs}{vector(character) - List of tfs consider. If NA, tfs are extracted |
|
|
28 |
from the hummus object with get_tfs function.} |
|
|
29 |
|
|
|
30 |
\item{gene_assay}{(character) - Name of the assay to get tfs from if tfs is |
|
|
31 |
not provided. If NULL, all TFs with motifs in the hummus object are used.} |
|
|
32 |
|
|
|
33 |
\item{method}{(character) - Method used to infer network edges. |
|
|
34 |
\itemize{ |
|
|
35 |
\item \code{'Omnipath'} - Use Omnipath to infer tf-tf networks. |
|
|
36 |
\item \code{'NULL'} - A fake connected network is computed. |
|
|
37 |
\item \code{'Other method'} - TO DO. |
|
|
38 |
}} |
|
|
39 |
|
|
|
40 |
\item{store_network}{(bool) - Save the network directly (\code{TRUE}, |
|
|
41 |
default) or return without saving on disk (\code{FALSE}).} |
|
|
42 |
|
|
|
43 |
\item{output_file}{(character) - Name of the output_file |
|
|
44 |
(if store_network == \code{TRUE}).} |
|
|
45 |
|
|
|
46 |
\item{source_target}{('AND'|'OR') - Fetch only the interactions involving |
|
|
47 |
two considered tfs (\code{'AND', default}), or one considered tfs and any |
|
|
48 |
other element (\code{'OR'})} |
|
|
49 |
|
|
|
50 |
\item{multiplex_name}{(character) - Name of the multiplex to add the network |
|
|
51 |
to. Default is \code{'TF'}.} |
|
|
52 |
|
|
|
53 |
\item{tf_network_name}{(character) - Name of the network in the multiplex to |
|
|
54 |
add the network to. Default is \code{'TF_network'}.} |
|
|
55 |
|
|
|
56 |
\item{verbose}{(integer) - Display function messages. Set to 0 for no message |
|
|
57 |
displayed, >= 1 for more details.} |
|
|
58 |
} |
|
|
59 |
\value{ |
|
|
60 |
(Hummus_Object) - Return hummus object with the new network added. |
|
|
61 |
} |
|
|
62 |
\description{ |
|
|
63 |
Compute a protein-protein interaction layer from Omnipath request that will represent tf cooperativity. |
|
|
64 |
This network is the top-layer of HuMMuS multilayer. |
|
|
65 |
} |
|
|
66 |
\examples{ |
|
|
67 |
hummus <- compute_tf_network(hummus, |
|
|
68 |
gene_assay = "RNA", |
|
|
69 |
verbose = 1) |
|
|
70 |
} |