Interpretation and enrichment for metabolomics data

---

Documentation for package ‘FELLA’ version 1.26.0

• 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