Table 2.
Classification Performance with Reference Transcripts of genus Arabidopsis
| Arabidopsis RNA | A Bowtie2 |
B Bo_AS |
C Bo_RF |
D STAR |
E St_AS |
F St_RF |
G Salmon |
H bwa |
|---|---|---|---|---|---|---|---|---|
| Accuracy | 72.7% | 81.0% | 95.0% | 73.0% | 80.9% | 88.5% | 70.8% | 75.2% |
| Sensitivity | 56.9% | 70.7% | 90.6% | 56.0% | 69.9% | 87.2% | 48.1% | 60.9% |
| Specificity | 88.5% | 91.3% | 99.5% | 90.0% | 91.9% | 89.9% | 93.5% | 89.0% |
| Precision | 83.2% | 89.1% | 99.4% | 84.9% | 89.6% | 89.6% | 88.0% | 84.7% |
| F1-score | 67.5% | 78.8% | 94.8% | 67.5% | 78.5% | 88.3% | 62.2% | 70.9% |
| MCC | 0.478 | 0.634 | 0.904 | 0.489 | 0.633 | 0.770 | 0.466 | 0.521 |
| AUPRC | – | – | 99.5% | – | – | 96.5% | – | – |
| AUROC | – | – | 99.4% | – | – | 96.2% | – | – |
| Pos Pref | 34.2% | 39.7% | 45.6% | 33.0% | 39.0% | 48.6% | 27.3% | 36.0% |
| Ties | – | 14.0% | – | – | 14.7% | – | – | – |
Performance metrics for parent-of-origin classification in Arabidopsis. In all seven approaches, RNA-seq read pairs were assigned to either of two reference transcriptomes. Whether used with Bowtie2 or STAR, the random forest method demonstrated superior performance. For the sake of directional statistics like sensitivity, species A. lyrata and A. halleri were designated as the negative and positive classes, respectively. (A) Parent chosen by the Bowtie2 aligner. (B) Parent chosen by comparing Bowtie2 alignment scores. (C) Parent chosen by the random forest classifier using Bowtie2 alignment features. (D, E, F) Similar to columns A, B, C, but using the STAR aligner, configured to avoid splicing. (G, H) Parent chosen by Salmon or bwa, respectively