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

In FELLA: Interpretation and enrichment for metabolomics data

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

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

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

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