private double calcPval(
HashMap<Integer, String> singleGeneCaseValueMap, String profileType, String profileStableId)
throws IllegalArgumentException {
double _p_value = 0.0;
if (profileType.equals(GeneticAlterationType.MUTATION_EXTENDED.toString())
|| profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())) {
_p_value = runFisherExactTest(singleGeneCaseValueMap, profileType);
} else if (profileType.equals(GeneticAlterationType.MRNA_EXPRESSION.toString())
|| profileType.equals(GeneticAlterationType.PROTEIN_LEVEL.toString())) {
_p_value = runTTest(singleGeneCaseValueMap, profileStableId);
}
return _p_value;
}
@Override
public ObjectNode process(long entrezGeneId, String[] values, ArrayList<Integer> sampleList) {
ObjectNode _datum = mapper.createObjectNode();
// create map to pair sample and value
HashMap<Integer, String> mapSampleValue = new HashMap<>();
for (int i = 0; i < values.length; i++) {
String value = values[i];
Integer sampleId = sampleList.get(i);
mapSampleValue.put(sampleId, value);
}
// remove empty entry
Iterator it = mapSampleValue.entrySet().iterator();
while (it.hasNext()) {
Map.Entry pair = (Map.Entry) it.next();
if (pair.getValue().equals("NA")
|| pair.getValue().equals("NaN")
|| pair.getValue().equals("null")) {
it.remove();
}
}
// get Gene Name and Cytoband
DaoGeneOptimized daoGeneOptimized = DaoGeneOptimized.getInstance();
String geneName = daoGeneOptimized.getGene(entrezGeneId).getHugoGeneSymbolAllCaps();
String cytoband = daoGeneOptimized.getGene(entrezGeneId).getCytoband();
// statistics analysis
if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())) {
if (!(Arrays.asList(queriedGenes)).contains(geneName)) { // remove queried genes from result
_datum.put(COL_NAME_GENE, geneName);
_datum.put(COL_NAME_CYTOBAND, cytoband);
_datum.put(
COL_NAME_PCT_ALTERED,
Integer.toString(countAltered(mapSampleValue, profileType, "altered"))
+ "////"
+ Double.toString(calcPct(mapSampleValue, profileType, "altered")));
_datum.put(
COL_NAME_PCT_UNALTERED,
Integer.toString(countAltered(mapSampleValue, profileType, "unaltered"))
+ "////"
+ Double.toString(calcPct(mapSampleValue, profileType, "unaltered")));
_datum.put(
COL_NAME_RATIO,
calcRatio(
calcPct(mapSampleValue, profileType, "altered"),
calcPct(mapSampleValue, profileType, "unaltered")));
_datum.put(COL_NAME_DIRECTION, "place holder"); // calculation is done by the front-end
_datum.put(COL_NAME_P_VALUE, calcPval(mapSampleValue, profileType, geneticProfileStableId));
if (!(calcPct(mapSampleValue, profileType, "altered") == 0.0
&& calcPct(mapSampleValue, profileType, "unaltered") == 0.0)
&& !Double.isNaN(calcPval(mapSampleValue, profileType, geneticProfileStableId))) {
return _datum;
}
}
} else if (profileType.equals(GeneticAlterationType.MRNA_EXPRESSION.toString())) {
_datum.put(COL_NAME_GENE, geneName);
_datum.put(COL_NAME_CYTOBAND, cytoband);
_datum.put(
COL_NAME_MEAN_ALTERED, calcMean(mapSampleValue, "altered", geneticProfileStableId));
_datum.put(
COL_NAME_MEAN_UNALTERED, calcMean(mapSampleValue, "unaltered", geneticProfileStableId));
_datum.put(
COL_NAME_STDEV_ALTERED, calcSTDev(mapSampleValue, "altered", geneticProfileStableId));
_datum.put(
COL_NAME_STDEV_UNALTERED, calcSTDev(mapSampleValue, "unaltered", geneticProfileStableId));
_datum.put(COL_NAME_P_VALUE, calcPval(mapSampleValue, profileType, geneticProfileStableId));
if (!Double.isNaN(calcPval(mapSampleValue, profileType, geneticProfileStableId))) {
return _datum;
}
} else if (profileType.equals(GeneticAlterationType.PROTEIN_LEVEL.toString())) {
_datum.put(COL_NAME_GENE, geneName);
_datum.put(COL_NAME_CYTOBAND, cytoband);
_datum.put(
COL_NAME_MEAN_ALTERED, calcMean(mapSampleValue, "altered", geneticProfileStableId));
_datum.put(
COL_NAME_MEAN_UNALTERED, calcMean(mapSampleValue, "unaltered", geneticProfileStableId));
_datum.put(
COL_NAME_STDEV_ALTERED, calcSTDev(mapSampleValue, "altered", geneticProfileStableId));
_datum.put(
COL_NAME_STDEV_UNALTERED, calcSTDev(mapSampleValue, "unaltered", geneticProfileStableId));
_datum.put(COL_NAME_P_VALUE, calcPval(mapSampleValue, profileType, geneticProfileStableId));
if (!Double.isNaN(calcPval(mapSampleValue, profileType, geneticProfileStableId))) {
return _datum;
}
}
return null;
}
