Change decoy generation to complementary

Use fixed npv Fix npv denominator
Nesvilab · May 29, 2024 · 776ec32 · 776ec32
1 parent 26ff7f2
commit 776ec32
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Showing 2 changed files with 11 additions and 10 deletions.
diff --git a/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java b/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
@@ -171,13 +171,13 @@ private void fitMatchedIonDistribution() throws Exception {
                             float[] reducedInts = reducedIons[1];
 
                             // Get sites that are/would be shifted
-                            ArrayList<Float> sitePepFrags = DownstreamPepFragGenerator.calculatePeptideFragments(
-                                    targetPep, this.ionTypes, mutationSite, 1);
-                            ArrayList<Float> decoySitePepFrags = DownstreamPepFragGenerator.calculatePeptideFragments(
-                                    decoyPep, this.ionTypes, mutationSite, 1);
+                            //ArrayList<Float> sitePepFrags = DownstreamPepFragGenerator.calculatePeptideFragments(
+                            //        targetPep, this.ionTypes, mutationSite, 1);
+                            //ArrayList<Float> decoySitePepFrags = DownstreamPepFragGenerator.calculatePeptideFragments(
+                            //        decoyPep, this.ionTypes, mutationSite, 1);
                             // Generate target and decoy fragments
-                            //ArrayList<Float> sitePepFrags = targetPep.calculatePeptideFragments(this.ionTypes, 1);
-                            //ArrayList<Float> decoySitePepFrags = decoyPep.calculateComplementaryFragments(this.ionTypes, mutatedMassShift, mutationSite, 1);
+                            ArrayList<Float> sitePepFrags = targetPep.calculatePeptideFragments(this.ionTypes, 1);
+                            ArrayList<Float> decoySitePepFrags = targetPep.calculateComplementaryFragments(this.ionTypes, mutatedMassShift, mutationSite, 1);
 
                             // Score over all possible sites
                             /**

diff --git a/src/edu/umich/andykong/ptmshepherd/iterativelocalization/MatchedIonDistribution.java b/src/edu/umich/andykong/ptmshepherd/iterativelocalization/MatchedIonDistribution.java
@@ -297,7 +297,7 @@ public void calculateNegativePredictiveValue() { // todo see if adding 1 here he
 
         this.ionPosterior = new double[((int) (100.0 * this.binMult + 1))];
         for (int i = 0; i < this.ionPosterior.length; i++) {
-            this.ionPosterior[i] = (double) ((this.pdf[i] + 1) / (double) (this.pdf[i] + this.pdfDecoy[i] + 2));
+            this.ionPosterior[i] = (double) ((this.pdf[i]) / (double) (this.pdf[i] + this.pdfDecoy[i]));
             System.out.println(this.ionPosterior[i]);
         }
         //this.negPredictiveValue = Math.max(this.negPredictiveValue, 0.01);
@@ -442,9 +442,10 @@ public double calcIonProbability(float intensity, float massError) {
     public double calculateIonProbabilityLda(float intensity, float massError) {
         double projVal;
         double prob;
-        if (intensity < 0)
-            prob = this.ionPosterior[(int) (intensity * -1 * this.binMult)];
-        else {
+        if (intensity < 0) {
+            //prob = this.ionPosterior[(int) (intensity * -1 * this.binMult)];
+            prob = this.negPredictiveValue;
+        } else {
             projVal = this.ldaProcessor.projectData(massError, intensity).getEntry(0,0);
             int projValIndex = translateLdaValToIndex(projVal);
             prob = 1.0 - this.qVals[projValIndex];