This mode is used to perform  univariate feature selection using the  Cox Regression test (the Cox proportional hazard model), We compare each feature individually for evidence of differential distribution in the two prediction classes. If the cox regression test p-value is less than the confidence interval, then the feature is selected as an informative biomarker.

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

Mode Parameters

The following options are available in this mode

Flag Arguments Required Description
(-n | --alpha)alphayesThe significance level for the univariate cox regression-test p-value. Default 0.05/5% confidence level. (default: 0.05)
--survivalsurvivalnoSurvival filename. This file contains survival data in tab delimited table; column 1: chipID has to match cids and tmm, column 2: time to event, column 3 censor with 1 as event 0 as censor, column 4 and beyond are all numerical covariates that will be included in the regression model
--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.