This repository contains the scripts implementing for the network inference method of the article (Marti-Marimon et al, 2018). It can be installed with:
devtools::install_github("tuxette/internet3D")
The main functions of the package are build.network
and bootstrap.build
.
After installation, supplementary files with the different networks described in the article are in:
system.file("results/network0.graphml", package = "internet3D")
(and similarly for network1
, network2
and network3
). They can be loaded within R with
library(igraph)
net0 <- system.file("results/network0.graphml", package = "internet3D")
net0 <- read_graph(net0, format = "graphml")
net0
## IGRAPH 99d2136 UN-- 359 2279 --
## + attr: name (v/c), id (v/c)
## + edges from 99d2136 (vertex names):
## [1] ABCB7 --ADAMTSL3 ABCB7 --CEND1 ABCB7 --COQ7 ABCB7 --FABP3
## [5] ABCB7 --HMGB2 ABCB7 --MGST3 ABCB7 --MITF ABCB7 --P2RX5
## [9] ABCB7 --PTMA ABCB7 --RAB3A ABCB7 --RBM10 ABCB7 --SELO
## [13] ABI3BP--COL16A1 ABI3BP--COL5A1 ABI3BP--DPYSL3 ABI3BP--HAUS1
## [17] ABI3BP--ITIH4 ABI3BP--NFATC3 ABI3BP--P4HA3 ABI3BP--RGS2
## [21] ABI3BP--SDC2 ABI3BP--ZHX1 ABR --ANXA3 ABR --ATP1B4
## [25] ABR --CAPN10 ABR --COL5A1 ABR --CRLF1 ABR --FGFR4
## [29] ABR --ISYNA1 ABR --ITGA9 ABR --LHX2 ABR --NFXL1
## + ... omitted several edges
The files are also directly accessible in this repository in inst/results
and can be read with any standard tool for graph visualization (e.g., Gephi, https://gephi.org/)
Marti-Marimon M., Villa-Vialaneix N., Voillet V., Yerle-Bouissou M., Lahbib-Mansais Y., Liaubet L. (2018) A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation. Preprint