org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.survival.kaplanmeier.metadata;
import org.biojava.nbio.survival.data.WorkSheet;
import java.util.ArrayList;
import java.util.LinkedHashMap;
/**
*
* @author Scooter Willis
*/
public class ClinicalMetaDataOutcome {
/**
*
* @param worksheet
* @param sensorMapColumn
* @param censorMap
* @param timeColumn
* @param timeScale
* @param metaDataInfoList
* @throws Exception
*/
static public void process(WorkSheet worksheet, String sensorMapColumn, LinkedHashMap censorMap, String timeColumn, Double timeScale, ArrayList metaDataInfoList) throws Exception {
for (MetaDataInfo metaDataInfo : metaDataInfoList) {
if (metaDataInfo.numeric) {
metaDataInfo.discreteQuantizer.process(worksheet, metaDataInfo.column);
}
metaDataInfo.setDiscreteValues(worksheet);
}
for (MetaDataInfo metaDataInfo : metaDataInfoList) {
int numberValues = metaDataInfo.getNumberDiscreteValues();
for(int i = 0; i < numberValues; i++){
}
}
}
/**
*
* @param args
*/
public static void main(String[] args) {
try {
LinkedHashMap censorMap = new LinkedHashMap<>();
censorMap.put("a", "0");
censorMap.put("d", "1");
censorMap.put("d-d.s.", "1");
censorMap.put("d-o.c.", "1");
String timeColumn = "TIME";
String sensorMapColumn = "last_follow_up_status"; // "survstat3";
double timeScale = 1.0;
ArrayList metaDataInfoList = new ArrayList<>();
metaDataInfoList.add(new MetaDataInfo("age_at_diagnosis", true, new MeanQuantizer()));
metaDataInfoList.add(new MetaDataInfo("size", true, new MeanQuantizer()));
metaDataInfoList.add(new MetaDataInfo("lymph_nodes_positive", true, new MeanQuantizer()));
metaDataInfoList.add(new MetaDataInfo("lymph_nodes_removed", true, new MeanQuantizer()));
metaDataInfoList.add(new MetaDataInfo("NPI", true, new MeanQuantizer()));
metaDataInfoList.add(new MetaDataInfo("menopausal_status_inferred"));
metaDataInfoList.add(new MetaDataInfo("group"));
metaDataInfoList.add(new MetaDataInfo("grade"));
metaDataInfoList.add(new MetaDataInfo("stage"));
metaDataInfoList.add(new MetaDataInfo("ER_IHC_status"));
metaDataInfoList.add(new MetaDataInfo("HER2_IHC_status"));
metaDataInfoList.add(new MetaDataInfo("HER2_SNP6_state"));
metaDataInfoList.add(new MetaDataInfo("cellularity"));
metaDataInfoList.add(new MetaDataInfo("P53_mutation_status"));
metaDataInfoList.add(new MetaDataInfo("P53_mutation_type"));
metaDataInfoList.add(new MetaDataInfo("Pam50Subtype"));
metaDataInfoList.add(new MetaDataInfo("Genefu"));
WorkSheet worksheet = WorkSheet.readCSV("/Users/Scooter/scripps/ngs/DataSets/METABRIC/EGAD00010000210/table_S2_revised.txt", '\t');
ClinicalMetaDataOutcome.process(worksheet, sensorMapColumn, censorMap, timeColumn, timeScale, metaDataInfoList);
} catch (Exception e) {
e.printStackTrace();
}
}
}