.params {FELLA} | R Documentation

## Dummy function with function arguments

### 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`

[Package FELLA version 1.2.0 Index]