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

Description Usage Arguments Value Slots

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

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## 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.