FELLA.USER: An S4 class to save all the user analysis data

In FELLA: Interpretation and enrichment for metabolomics 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

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