update variable name convention on BenjaminHochberg.java
@@ -24,7 +24,7 @@ import java.util.HashMap;
public class BenjaminHochberg {
- private ArrayList<Double> pvalueList = new ArrayList<>();
+ private ArrayList<Double> pValueList = new ArrayList<>();
private ArrayList<Double> indexList = new ArrayList<>();
private ArrayList<String> fdrList = new ArrayList<>();
@@ -36,23 +36,23 @@ public class BenjaminHochberg {
double star = 0.05, doubleStar = 0.01;
for (int i = 0; i < totalGo; i++) {
- pvalueList.add((double)pvalues[i] / (double)miRNA_groups);
+ pValueList.add((double)pvalues[i] / (double)miRNA_groups);
indexList.add((double)pvalues[i] / (double)miRNA_groups);
fdrList.add("");
}
for (int i = 0; i < totalNoGo; i++) {
- pvalueList.add(1.0);
+ pValueList.add(1.0);
indexList.add(1.0);
fdrList.add("");
}
- Collections.sort(pvalueList);
- int pNodeListSize = pvalueList.size();
+ Collections.sort(pValueList);
+ int pNodeListSize = pValueList.size();
for (int i = 0; i < pNodeListSize; i++) {
double starcheck = (double)(((i + 1) * star)) / (double)pNodeListSize;
- if (pvalueList.get(i) <= starcheck) {
+ if (pValueList.get(i) <= starcheck) {
maxI = i;
}
}
@@ -67,7 +67,7 @@ public class BenjaminHochberg {
for (int i = 0; i < pNodeListSize; i++) {
double starcheck = (double)((i + 1) * doubleStar) / (double)pNodeListSize;
- if (pvalueList.get(i) <= starcheck) {
+ if (pValueList.get(i) <= starcheck) {
maxI = i;
}
}
@@ -80,12 +80,12 @@ public class BenjaminHochberg {
fdrList.set(i,"**");
}
- pvalueList = indexList;
+ pValueList = indexList;
}
public ArrayList<Double> returnPvalueList() {
- return pvalueList;
+ return pValueList;
}
public ArrayList<String> returnFdrList() {
