dot-params: Dummy function with function arguments

In FELLA: Interpretation and enrichment for metabolomics data

Description

This function eases parameter inheritance to centralise the documentation

Usage

.params()

Arguments

databaseDir	Path for the KEGG RData files
internalDir	Logical, is the directory located in the package directory?
object	FELLA.USER object
data	FELLA.DATA object
type	Character vector, containing entries in "hypergeom", "diffusion" or "pagerank"
level	Desired level, can be coded as a number or a character: 1 or "pathway"; 2 or "module"; 3 or "enzyme"; 4 or "reaction"; 5 or "compound".
method	Character, exactly one of: "hypergeom", "diffusion", "pagerank"
methods	Character vector, containing some of: "hypergeom", "diffusion", "pagerank"
approx	Character: "simulation" for Monte Carlo, "normality", "gamma" or "t" for parametric approaches
loadMatrix	Character vector to choose if heavy matrices should be loaded. Can contain: "diffusion", "pagerank"
threshold	Numeric value between 0 and 1. p.score threshold applied when filtering KEGG nodes. Lower thresholds are more stringent.
thresholdConnectedComponent	Numeric value between 0 and 1. Connected components that are below the threshold are kept, while the ones exceeding it (because they are too small) are discarded.
plimit	Pathway limit, must be a numeric value between 1 and 50. Limits the amount of pathways in method = "hypergeom"
nlimit	Node limit, must be a numeric value between 1 and 1000. Limits the order of the solution sub-graph when in method = "diffusion" and method = "pagerank"
niter	Number of iterations (permutations) for Monte Carlo ("simulation"), must be a numeric value between 1e2 and 1e5
layout	Logical, should the plot be returned as a layout?
graph	An igraph object, typically a small one, coming from an enrichment through "diffusion" or "pagerank".
GOterm	Character, GO entry to draw semantic similarity in the solution graph. If NULL, the GO labels will be appended without similarities.
GONamesAsLabels	Logical, should GO names be displayed as labels instead of GO identifiers?
LabelLengthAtPlot	Numeric value between 10 and 50. Maximum length that a label can reach when plotting the graph. The remaining characters will be truncated using "..."
godata.options	List, options for the database creator godata
mart.options	List, options for the biomaRt function getBM. Importantly, this defines the organism, see listDatasets for possibilities. If calling generateEnzymesTable, the user can set mart.options = NULL to avoid adding GO labels to enzymes.
p.adjust	Character passed to the p.adjust method
dampingFactor	Numeric value between 0 and 1 (none inclusive), damping factor d for PageRank (page.rank)
t.df	Numeric value; number of degrees of freedom of the t distribution if the approximation approx = "t" is used
compounds	Character vector containing the KEGG IDs of the compounds considered as affected
compoundsBackground	Character vector containing the KEGG IDs of the compounds that belong to the background. Can be NULL for the default background (all compounds)
NamesAsLabels	Logical, should KEGG names be displayed as labels instead of KEGG identifiers?
capPscores	Numeric value, minimum p-score admitted for the readable formatting. Smaller p-scores will be displayed as < capPscores

Value

NULL

FELLA documentation built on Nov. 8, 2020, 6:57 p.m.