Description Usage Arguments Value Examples
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.
1 2 3 4 5 6 7  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"), ...)

databaseDir 
Path for the KEGG RData files 
internalDir 
Logical, is the directory located in the package directory? 
method 
Character, exactly one of:

methods 
Character vector, containing some of:

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: 
threshold 
Numeric value between 0 and 1.

plimit 
Pathway limit, must be a numeric value between 1 and 50.
Limits the amount of pathways in 
nlimit 
Node limit, must be a numeric value between 1 and 1000.
Limits the order of the solution subgraph when
in 
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 
dampingFactor 
Numeric value between 0 and 1 (none inclusive),
damping factor 
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 
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 
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).
1 2 3 4 5  ## This function is internal
arg1 < FELLA:::checkArguments(method = "hello")
arg1$valid
arg2 < FELLA:::checkArguments(method = "diffusion")
arg2$valid

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