checkArguments {FELLA} | R Documentation |
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.
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 sub-graph 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).
## This function is internal arg1 <- FELLA:::checkArguments(method = "hello") arg1$valid arg2 <- FELLA:::checkArguments(method = "diffusion") arg2$valid