checkArguments: Internal function to check arguments and give personalised...

Description Usage Arguments Value Examples

View source: R/AllArguments.R

Description

This function checks if the arguments are of the desired type, length and range. If it fails, it gives an error explaining why the argument is invalid.

Usage

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checkArguments(databaseDir = "myDatabase", internalDir = TRUE,
    method = "diffusion", methods = "diffusion", approx = "normality",
    loadMatrix = NULL, threshold = 0.05, plimit = 15, nlimit = 250,
    niter = 1000, t.df = 10, dampingFactor = 0.85, layout = FALSE,
    thresholdConnectedComponent = 0.05, GOterm = NULL,
    GONamesAsLabels = TRUE, LabelLengthAtPlot = 22,
    object = new("FELLA.USER"), data = new("FELLA.DATA"), ...)

Arguments

databaseDir

Path for the KEGG RData files

internalDir

Logical, is the directory located in the package directory?

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.

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

t.df

Numeric value; number of degrees of freedom of the t distribution if the approximation approx = "t" is used

dampingFactor

Numeric value between 0 and 1 (none inclusive), damping factor d for PageRank (page.rank)

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.

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 "..."

object

FELLA.USER object

data

FELLA.DATA object

...

ignored arguments

Value

A list with values. Currently only a logical value named valid if the process runs smoothly. If the checking fails, it also returns an object called ans, which depends on the situation (can be the original object, NULL, et cetera).

Examples

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## This function is internal
arg1 <- FELLA:::checkArguments(method = "hello")
arg1$valid
arg2 <- FELLA:::checkArguments(method = "diffusion")
arg2$valid

b2slab/FELLA documentation built on March 3, 2021, 2:22 p.m.