add unit tests for duplicitiy

Author: tonywu1999

inst/tinytest/test_utils_anomaly_score.R

@@ -367,3 +367,21 @@ low_abundance_excluded = MSstatsConvert:::.prepareSpectronautAnomalyInput(
     missing_run_count = 0.95)
 expect_true("AFPLAEWQPSDVDQR" %in% low_abundance_excluded$PeptideSequence)
 expect_false("LowAbundancePeptide" %in% low_abundance_excluded$PeptideSequence)
+
+
+# Test 11: Testing duplicity of quality metrics, applicable considering
+# multiple fragments share the same precursor level metrics
+
+# Data with progressively higher cumulative sums
+duplicate_metrics = run_quality_metrics(
+    base_df_10,
+    c(rep(0.1, 5), seq(2.0, 4.0, length.out = 5)),  # mean_increase
+    c(rep(0.1, 5), seq(2.0, 4.0, length.out = 5)),  # mean_decrease
+    c(rep(0.1, 5), seq(2.0, 4.0, length.out = 5))   # dispersion_increase
+)
+
+# The last 5 rows (with high values) should have lower mean anomaly scores
+# Since they are all clumped between 2 and 4, whereas 0.1 is by itself
+expect_true(mean(duplicate_metrics$AnomalyScores[6:10]) < mean(duplicate_metrics$AnomalyScores[1:5]),
+            info = "Rows 6-10 (values clumped 2-4) should have lower 
+            anomaly scores than rows 1-5 (isolated value of 0.1)")