Package org.biojava.nbio.survival.cox

Class CoxHelper

java.lang.Object

org.biojava.nbio.survival.cox.CoxHelper

public class CoxHelper
extends Object

The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class. Given the number of options for adjusting the calculations using weighting, strata, clustering etc the helper class can be used to hide the complexity for typical use case.

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
CoxHelper()

Method Summary

Modifier and Type	Method	Description
static void	main(String[] args)
static CoxInfo	process(String datafile, String timeColumn, String statusColumn, String weightColumn, String strataColumn, String clusterColumn, ArrayList<String> variables, boolean useStrata, boolean useWeights)
static CoxInfo	process(WorkSheet worksheet, String timeColumn, String statusColumn, String weightColumn, String strataColumn, String clusterColumn, ArrayList<String> variables, boolean useStrata, boolean useWeights)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CoxHelper

public CoxHelper()

Method Detail

process

public static CoxInfo process(String datafile,
                              String timeColumn,
                              String statusColumn,
                              String weightColumn,
                              String strataColumn,
                              String clusterColumn,
                              ArrayList<String> variables,
                              boolean useStrata,
                              boolean useWeights)
                       throws Exception

Parameters:

datafile - The tab delimited file containing survival data and variables. The first column needs to be unique index

timeColumn - The column representing the event/censor time

statusColumn - The column representing an event=1 and censor=0

weightColumn - For case-cohort data sets may require weighting to reflect the entire cohort

strataColumn - A column representing strata data

clusterColumn - If robost variation calculation is required the cluster column will group samples by the value in this column

variables - The variables to be used in the cox regression analysis. For Interactions using variable1:variable2

useStrata - Boolean to indicate if strata column should be used

useWeights - Boolean to indicate if weight column should be used

Returns:

Throws:

Exception

process

public static CoxInfo process(WorkSheet worksheet,
                              String timeColumn,
                              String statusColumn,
                              String weightColumn,
                              String strataColumn,
                              String clusterColumn,
                              ArrayList<String> variables,
                              boolean useStrata,
                              boolean useWeights)

Parameters:

worksheet -

timeColumn - The column representing the event/censor time

statusColumn - The column representing an event=1 and censor=0

weightColumn - For case-cohort data sets may require weighting to reflect the entire cohort

strataColumn - A column representing strata data

clusterColumn - If robost variation calculation is required the cluster column will group samples by the value in this column

variables - The variables to be used in the cox regression analysis. For Interactions using variable1:variable2

useStrata - Boolean to indicate if strata column should be used

useWeights - Boolean to indicate if weight column should be used

Returns:

main

public static void main(String[] args)

Parameters:

args - the command line arguments