R: An S4 class to save all the user analysis data

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]