|
a |
|
b/man/define_binding_regions.Rd |
|
|
1 |
% Generated by roxygen2: do not edit by hand |
|
|
2 |
% Please edit documentation in R/explore_network.R |
|
|
3 |
\name{define_binding_regions} |
|
|
4 |
\alias{define_binding_regions} |
|
|
5 |
\title{Define binding_regions from hummus object} |
|
|
6 |
\usage{ |
|
|
7 |
define_binding_regions( |
|
|
8 |
hummus_object, |
|
|
9 |
multiplex_names = NULL, |
|
|
10 |
bipartites_names = NULL, |
|
|
11 |
config_name = "binding_regions_config.yml", |
|
|
12 |
config_folder = "config", |
|
|
13 |
tf_multiplex = "TF", |
|
|
14 |
atac_multiplex = "peaks", |
|
|
15 |
rna_multiplex = "RNA", |
|
|
16 |
multilayer_f = "multilayer", |
|
|
17 |
gene_list = NULL, |
|
|
18 |
tf_list = NULL, |
|
|
19 |
save = FALSE, |
|
|
20 |
output_f = NULL, |
|
|
21 |
return_df = TRUE, |
|
|
22 |
suffix_bipartites = ".tsv", |
|
|
23 |
njobs = 1 |
|
|
24 |
) |
|
|
25 |
} |
|
|
26 |
\arguments{ |
|
|
27 |
\item{hummus_object}{A hummus object} |
|
|
28 |
|
|
|
29 |
\item{multiplex_names}{A vector of multiplex names considered. |
|
|
30 |
It must be a subset of the names of the multiplexes in the hummus object.} |
|
|
31 |
|
|
|
32 |
\item{bipartites_names}{A vector of bipartites names considered. |
|
|
33 |
It must be a subset of the names of the bipartites in the hummus object.} |
|
|
34 |
|
|
|
35 |
\item{config_name}{The name of the config file to be created by hummuspy} |
|
|
36 |
|
|
|
37 |
\item{config_folder}{The folder where the config file will be created} |
|
|
38 |
|
|
|
39 |
\item{tf_multiplex}{The name of the multiplex containing the TFs} |
|
|
40 |
|
|
|
41 |
\item{atac_multiplex}{The name of the multiplex containing the ATAC-seq peaks} |
|
|
42 |
|
|
|
43 |
\item{rna_multiplex}{The name of the multiplex containing the RNA-seq genes} |
|
|
44 |
|
|
|
45 |
\item{multilayer_f}{The folder where the multilayer is stored} |
|
|
46 |
|
|
|
47 |
\item{gene_list}{A vector of genes to be considered for the final binding |
|
|
48 |
regions (filtering is done on the genes before inferring the binding_regions)} |
|
|
49 |
|
|
|
50 |
\item{tf_list}{A vector of TFs to be considered for the binding_regions |
|
|
51 |
(filtering is done on the TFs after inferring the binding_regions)} |
|
|
52 |
|
|
|
53 |
\item{save}{A boolean indicating if the binding_regions should be saved} |
|
|
54 |
|
|
|
55 |
\item{output_f}{The name of the file where the binding_regions can be saved |
|
|
56 |
(if save == TRUE)} |
|
|
57 |
|
|
|
58 |
\item{return_df}{A boolean indicating if the binding_regions should be |
|
|
59 |
returned as a dataframe} |
|
|
60 |
|
|
|
61 |
\item{suffix_bipartites}{A suffix to add to the bipartites names (to indicate |
|
|
62 |
the exact file location)} |
|
|
63 |
|
|
|
64 |
\item{njobs}{The number of jobs to be used for the computation of the binding_regions} |
|
|
65 |
} |
|
|
66 |
\value{ |
|
|
67 |
A dataframe containing the binding_regions (if return_df == TRUE) |
|
|
68 |
} |
|
|
69 |
\description{ |
|
|
70 |
Calling the define_output function with output_type = 'binding_regions' |
|
|
71 |
} |
|
|
72 |
\examples{ |
|
|
73 |
binding_regions <- define_binding_regions(hummus_object = hummus, |
|
|
74 |
multilayer_f = multilayer_folder, |
|
|
75 |
njobs = 5) |
|
|
76 |
|
|
|
77 |
} |