# Interpretation and enrichment for metabolomics data

## Documentation for package ‘FELLA’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

FELLA-package | The FELLA package
addGOToGraph | Generate and manipulate tables and sub-networks from an enrichment
buildDataFromGraph | Parse, build and load the KEGG knowledge model
buildGraphFromKEGGREST | Parse, build and load the KEGG knowledge model
D.diffusion-class | An internal S4 class for the diffusion data
D.hypergeom-class | An internal S4 class for the binary matrix (hypergeometric test)
D.keggdata-class | An internal S4 class to represent the KEGG graph and related files
D.pagerank-class | An internal S4 class for the PageRank data
data-funs | Parse, build and load the KEGG knowledge model
defineCompounds | Functions to map and enrich a list of metabolites
enrich | Functions to map and enrich a list of metabolites
enrich-funs | Functions to map and enrich a list of metabolites
export-funs | Generate and manipulate tables and sub-networks from an enrichment
exportResults | Generate and manipulate tables and sub-networks from an enrichment
FELLA | The FELLA package
FELLA.DATA | An S4 class to represent all the necessary KEGG data
FELLA.DATA-class | An S4 class to represent all the necessary KEGG data
FELLA.sample | FELLA.DATA sample data
FELLA.USER | An S4 class to save all the user analysis data
FELLA.USER-class | An S4 class to save all the user analysis data
generateEnzymesTable | Generate and manipulate tables and sub-networks from an enrichment
generateResultsGraph | Generate and manipulate tables and sub-networks from an enrichment
generateResultsTable | Generate and manipulate tables and sub-networks from an enrichment
getBackground | Get compounds in the defined background
getCom | Get community
getExcluded | Get excluded compounds
getGraph | Get KEGG graph
getInfo | Get KEGG version info
getInput | Get metabolites in the input
getMatrix | Get matrix for the desired methodology
getName | Map KEGG identifiers to KEGG names
getPscores | Get p-scores from the desired methodology
getStatus | Get the slot "status"
getSums | Get rowSums/squaredRowSums
getValid | Get the slot "valid"
input.sample | A randomly generated list of affected metabolites
is.FELLA.DATA | Check FELLA.DATA class
is.FELLA.USER | Check FELLA.USER class
launchApp | Launch a shiny app with FELLA
listApprox | List of approximations
listCategories | List of node categories
listInternalDatabases | List internal databases
listMethods | List of methods
loadKEGGdata | Parse, build and load the KEGG knowledge model
plot-method | An S4 class to save all the user analysis data
plotGraph | Generate and manipulate tables and sub-networks from an enrichment
plotLegend | Internal function to add a legend to a graph plot
runDiffusion | Functions to map and enrich a list of metabolites
runHypergeom | Functions to map and enrich a list of metabolites
runPagerank | Functions to map and enrich a list of metabolites
show-method | An S4 class to represent all the necessary KEGG data
show-method | An S4 class to save all the user analysis data
U.diffusion-class | An internal S4 class for the user data of the diffusion enrichment analysis
U.hypergeom-class | An internal S4 class for the user data of the hypergeometric over representation analysis
U.pagerank-class | An internal S4 class for the user data of the PageRank enrichment analysis
U.userinput-class | An internal S4 class for the user input data