FELLA.USER-class {FELLA} | R Documentation

## An S4 class to save all the user analysis data

### Description

Assigning the value of show to a variable will provide small data frames with the best scoring pathways (`hypergeom`) and the best nodes in the KEGG network (`diffusion` and `pagerank`)

### Usage

    ## S4 method for signature 'FELLA.USER'
    show(object)

    ## S4 method for signature 'FELLA.USER,missing'
    plot(x = new("FELLA.USER"),
        method = "hypergeom", threshold = 0.05, plimit = 15,
        nlimit = 250, layout = FALSE, thresholdConnectedComponent = 0.05,
        LabelLengthAtPlot = 22, data = NULL, ...)

### Arguments

`object` | A `FELLA.USER` object
`x` | A `FELLA.USER` object
`method` | Character, exactly one of: `"hypergeom"`, `"diffusion"`, `"pagerank"`
`threshold` | Numeric value between 0 and 1. `p.score` threshold applied when filtering KEGG nodes. Lower thresholds are more stringent.
`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"`
`layout` | Logical, should the plot be returned as a layout?
`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.
`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 "..."
`data` | FELLA.DATA object
`...` | Additional arguments passed to plotting functions

### Value

`show` invisibly returns a list of data frames with the best hits for each applied method

`plot` returns a layout if `layout = T`, otherwise `invisible()`

### Slots

`userinput`

  A `U.userinput` S4 object

`hypergeom`

  A `U.hypergeom` S4 object

`diffusion`

  A `U.diffusion` S4 object

`pagerank`

  A `U.pagerank` S4 object

[Package FELLA version 1.2.0 Index]