This mode is used to perform univariate feature selection with a permutation Test. We compare each feature individually for evidence of differential distribution in the two prediction classes.  If the adhoc test statistic p-value is less than the confidence interval, then the feature is selected as an informative biomarker.

It is implemented by org.bdval.DiscoverWithPermutation.java.

Mode Parameters

The following options are available in this mode

Flag Arguments Required Description
(-n|--alpha)alphayesThe significance level for the permutation test p-value. Default 0.05/5% confidence level. (default: 0.05)
(-z|--numberOfPermutations)numberOfPermutationsyesThe number of permutation iterations. Default 1000. (default: 1000)
--output-gene-listn/anoWrite features to the output in the tissueinfo gene list format.
--report-max-probesreport-max-probesnoRestrict output to the top ranked probes. This option works in conjunction with alpha and can further restrict the output.