dot-params: Dummy function with function arguments

Description Usage Arguments Value

Description

This function eases parameter inheritance to centralise the documentation

Usage

1

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.