Table 4.
The recalls of annotating the PBMCs using scMatch and SingleR using ENCODE, BLUEPRINT and HPCA datasets
| BLUEPRINT+ENCODE |
HPCA |
BLUEPRINT+ENCODE +HPCA |
BLUEPRINT+ENCODE +HPCA+FANTOM5 | ||||
|---|---|---|---|---|---|---|---|
| SingleR (%) | scMatch (%) | SingleR (%) | scMatch (%) | SingleR (%) | scMatch (%) | scMatch (%) | |
| CD4+/CD25+ Regulatory T cells | 42.8 | 28.1 | 0.0 | 0.0 | 43.1 | 37.9 | 39.0 |
| CD8+ Cytotoxic T cells | 82.7 | 27.5 | 18.0 | 8.9 | 34.0 | 43.0 | 44.8 |
| CD19+ B cells | 99.9 | 66.5 | 100.0 | 99.9 | 90.5 | 99.0 | 99.2 |
| CD56+ NK cells | 99.2 | 95.8 | 95.1 | 93.3 | 95.0 | 98.4 | 98.5 |
| CD4+ Helper T cells | 94.5 | 86.4 | 99.5 | 99.5 | 93.5 | 98.2 | 97.9 |
| CD14+ Monocytes | 98.1 | 95.5 | 83.2 | 95.6 | 96.4 | 97.6 | 97.7 |
| CD34+ cells | 84.6 | 88.2 | 80.4 | 85.3 | 88.5 | 85.7 | 85.3 |
| CD4+/CD45RO+ Memory T cells | 75.4 | 80.8 | 95.3 | 97.5 | 73.1 | 86.8 | 86.0 |
| CD4+/CD45RA+/CD25− Naive T cells | N/A | N/A | 85.3 | 85.3 | 0.0 | 0.0 | 0.0 |
| CD8+/CD45RA+ Naive Cytotoxic T cells | N/A | N/A | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
Note: Comparison of scMatch and SingleR using different reference datasets. Annotation recall is calculated as in Table 3. (i) We used SingleR in fine-tuning mode, (ii) There are no matched reference samples in the BLUEPRINT + ENCODE database for CD4+/CD45RA+/CD25− Naïve T cells and CD8+/CD45RA+ Naïve cytotoxic T cells.