@Override
public void initOptions() {
// parent options
super.initOptions();
// mode
options.addOption(
OptionFactory.createOption(
"method", "Gene set analysis method [fatiscan, logistic]", false, true));
// list 1
options.addOption(
OptionFactory.createOption("ranked-list", "the feature data containig the ranked list"));
// test
options.addOption(
OptionFactory.createOption("partitions", "the number of partitions", false, true));
// extras
options.addOption(
OptionFactory.createOption(
"output-format",
"short (just most significant partition) or long (term results for all partitions) [short]",
false,
true));
options.addOption(
OptionFactory.createOption("order", "ascend or descend [ascend]", false, true));
options.addOption(
OptionFactory.createOption(
"higher-label", "label for condition with higher statistical values", false, true));
options.addOption(
OptionFactory.createOption(
"lower-label", "label for condition with lower statistical values", false, true));
options.addOption(OptionFactory.createOption("duplicates", "to remove duplicated IDs", false));
}
@Override
public void initOptions() {
options.addOption(OptionFactory.createOption("dataset", "the data"));
options.addOption(OptionFactory.createOption("class-name", "class"));
options.addOption(OptionFactory.createOption("class-values", "value"));
options.addOption(OptionFactory.createOption("test", "test: t, limma, anova, fold_change"));
options.addOption(
OptionFactory.createOption(
"correction",
"Multiple-test correction: fdr, bh, by, bonferroni, hochberg, hold",
false));
options.addOption(
OptionFactory.createOption("p-value", "p-value for significative genes", false));
options.addOption(
OptionFactory.createOption(
"fold-change-value", "fold-change for significative genes", false));
// options.addOption(OptionFactory.createOption("batch", "class class variable"));
}