onParameters <- function(method="L1", constraint=0.05, multiassay=c("singleassay", "multiassay", "multiassayPerChannel", "multiassayWithReferenceChannel"), referenceChannel=c("1","2"), ..., pluginVersion="0.5") {
#### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#L+# Checking plugin version
#### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (compareVersion(pluginVersion, "0.5") > 0)
throw("Requested plugin version is not available: ", pluginVersion);
if (compareVersion(pluginVersion, "0.5") < 0)
throw("Requested plugin version is too old: ", pluginVersion);
#L-#
#### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#L+# Pre-processing plugin parameters
#### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'methods':
validValues <- eval(formals(normalizeAffine.matrix)[["method"]]);
method <- match.arg(method, validValues);
# Argument 'bandwidth':
constraint <- as.double(constraint);
if (is.na(constraint))
throw("Parameter 'constraint' is NA.");
if (constraint <= 0)
constraint <- 0.05;
# Argument 'multiassay':
multiassay <- match.arg(multiassay);
# Argument 'referenceChannel':
referenceChannel <- unlist(strsplit(referenceChannel, split="[\t, ]"));
referenceChannel <- as.integer(referenceChannel);
if (any(is.na(referenceChannel))) {
throw("Parameter 'referenceChannel' is NA: ",
paste(referenceChannel, collapse=", "));
}
if (any(referenceChannel < 1 | referenceChannel > 2)) {
throw("Parameter 'referenceChannel' is out of range: ",
paste(referenceChannel, collapse=", "));
}
#L-#
# Return updated plugin parameters
list(
method=method,
constraint=constraint,
multiassay=multiassay,
referenceChannel=referenceChannel
);
}
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