private double calcMean(
HashMap<Integer, String> singleGeneCaseValueMap,
String groupType,
String profileStableId) { // group type: altered or unaltered
switch (groupType) {
case "altered":
int _index_altered = 0;
double[] alteredArray = new double[alteredSampleIds.size()];
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
alteredArray[_index_altered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
alteredArray[_index_altered] =
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_altered += 1;
}
}
return StatUtils.mean(alteredArray);
case "unaltered":
int _index_unaltered = 0;
double[] unalteredArray = new double[unalteredSampleIds.size()];
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
unalteredArray[_index_unaltered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
unalteredArray[_index_unaltered] =
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_unaltered += 1;
}
}
return StatUtils.mean(unalteredArray);
default:
return Double.NaN; // error
}
}
private double runTTest(HashMap<Integer, String> singleGeneCaseValueMap, String profileStableId)
throws IllegalArgumentException {
double[] unalteredArray = new double[unalteredSampleIds.size()];
double[] alteredArray = new double[alteredSampleIds.size()];
int _index_unaltered = 0, _index_altered = 0;
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
alteredArray[_index_altered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
alteredArray[_index_altered] =
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_altered += 1;
}
}
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
unalteredArray[_index_unaltered] =
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2);
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
unalteredArray[_index_unaltered] =
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
_index_unaltered += 1;
}
}
if (alteredArray.length < 2 || unalteredArray.length < 2) return Double.NaN;
else {
double pvalue = TestUtils.tTest(alteredArray, unalteredArray);
return pvalue;
}
}
private double calcSTDev(
HashMap<Integer, String> singleGeneCaseValueMap, String groupType, String profileStableId) {
switch (groupType) {
case "altered":
DescriptiveStatistics stats_altered = new DescriptiveStatistics();
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_altered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_altered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_altered.getStandardDeviation();
case "unaltered":
DescriptiveStatistics stats_unaltered = new DescriptiveStatistics();
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_unaltered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_unaltered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_unaltered.getStandardDeviation();
default:
return Double.NaN; // error
}
}
private double runFisherExactTest(
HashMap<Integer, String> singleGeneCaseValueMap, String profileType) {
int a = 0, // non altered
b = 0, // x non altered, y altered
c = 0, // x altered, y non altered
d = 0; // both alered
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())) {
try {
Double value = Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId));
if (copyNumType.equals("del")) {
if (value == -2.0) {
d += 1;
} else {
c += 1;
}
} else if (copyNumType.equals("amp")) {
if (value == 2.0) {
d += 1;
} else {
c += 1;
}
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else if (profileType.equals(GeneticAlterationType.MUTATION_EXTENDED.toString())) {
String value = singleGeneCaseValueMap.get(alteredSampleId);
if (value.equals("Non")) {
c += 1;
} else {
d += 1;
}
}
}
}
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())) {
try {
Double value = Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId));
if (copyNumType.equals("del")) {
if (value == -2.0) {
b += 1;
} else {
a += 1;
}
} else if (copyNumType.equals("amp")) {
if (value == 2.0) {
b += 1;
} else {
a += 1;
}
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else if (profileType.equals(GeneticAlterationType.MUTATION_EXTENDED.toString())) {
String value = singleGeneCaseValueMap.get(unalteredSampleId);
if (value.equals("Non")) {
a += 1;
} else {
b += 1;
}
}
}
}
FisherExact fisher = new FisherExact(a + b + c + d);
return fisher.getCumlativeP(a, b, c, d);
}
private double calcPct(
HashMap<Integer, String> singleGeneCaseValueMap,
String profileType,
String groupType) { // group type: altered or unaltered
double _result_pct = 0, _count = 0; // altered samples count
if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())
&& copyNumType.equals("del")) {
switch (groupType) {
case "altered":
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)) == -2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / alteredSampleIds.size();
break;
case "unaltered":
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)) == -2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / unalteredSampleIds.size();
break;
}
} else if (profileType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION.toString())
&& copyNumType.equals("amp")) {
switch (groupType) {
case "altered":
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)) == 2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / alteredSampleIds.size();
break;
case "unaltered":
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
try {
if (Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)) == 2.0) {
_count += 1;
}
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
_result_pct = _count / unalteredSampleIds.size();
break;
}
} else if (profileType.equals(GeneticAlterationType.MUTATION_EXTENDED.toString())) {
switch (groupType) {
case "altered":
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (!singleGeneCaseValueMap.get(alteredSampleId).equals("Non")) {
_count += 1;
}
}
}
_result_pct = _count / alteredSampleIds.size();
break;
case "unaltered":
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (!singleGeneCaseValueMap.get(unalteredSampleId).equals("Non")) {
_count += 1;
}
}
}
_result_pct = _count / unalteredSampleIds.size();
break;
}
}
return _result_pct;
}