Enriching metabolomics data through diffusion

This repository contains the FELLA package. FELLA is a metabolomics data enrichment tool that contextualises the experimental results using KEGG reactions, enzymes, modules and pathways.

• The input for our package is a list of affected metabolites between experimental conditions.
• The layout of the analysis is in a comprehensive human-readable layout, exportable to several formats, containing a biological interpetation of the experiment.

The subnetwork displayed to the user is found using diffusive processes on a graph that represents the known biological annotations at several molecular levels. To use this package type in your terminal:

R CMD build FELLA
R CMD INSTALL FELLA

Alternatively, you can use devtools if you experience some trouble building the vignette. Working in the package directory, this should do the trick:

devtools::install(build_vignettes = T)

Once FELLA is installed, you may load it by typing in your R terminal

library("FELLA")

To get the global picture about FELLA usage, you may browse its vignette

browseVignettes("FELLA")

All of the functions in FELLA have a (very basic) documentation, inclusive the package and the sample data FELLA.sample and input.sample.

In addition, there is a shiny app to facilitate the usage of the package. Before launching it, a database should be built. For example, for Homo sapiens excluding the hsa01100 pathway:

g <- buildGraphFromKEGGREST(
  organism = "hsa", 
  filter.path = "hsa01100"
)
buildDataFromGraph(g)

Then we can launch the shiny app

FELLA:::launchApp(
  host = "127.0.0.1", 
  port = 8888
)

and leave the command active. Going to the direction http://127.0.0.1:8888 will start the analysis.