Example #1
0
 @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));
 }
Example #2
0
 @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"));
 }