In montilab/bieulergy: Interactive analysis of multi-omics regulatory networks

knitr::opts_chunk$set(message=FALSE, warning=FALSE)
devtools::load_all()
options(width=600)

Uploading Custom Networks

Bieulergy optimizes performance by representing networks as node/edge-lists and pre-computing various graph statistics used throughout the application. User data can be uploaded in the form of a serialized R object file .rds. The object must be a named list of one or more interactive network objects.

Please refer to our documentation for creating interactive network objects.

Bieulergy assumes the following:

• Networks are represented as gene x gene adjacency matrices with edges present in the upper triangle
• Networks are undirected
• Networks are the same dimensions and share the same row/column names

Example

Here is an example of how the data should be formatted with 5 simulated networks of 100 genes.

upload <- readRDS(file.path(system.file("extdata", package="bieulergy"), "yeast-networks.rds"))

A list of interactive omics objects...

is(upload)

sapply(upload, is)

Some pre-computed graph measures...

print(upload$`Yeast #1`$properties)
head(upload$`Yeast #1`$nodes)

montilab/bieulergy documentation built on March 25, 2022, 3:40 p.m.