Table 5 Inclusion of random effect to increase discovery power of sc-eQTL mapping in Smart-Seq2 iPSC scRNA-seq data. Shown are the number of eGenes that are discovered at an FDR of 5% and the replication in all bulk (a-bulk) defined as FDR < 10% and same sign. Tested are the expressed genes on chromosome 2 matched between the two considered aggregations (d-mean and dr-mean, n genes = 20,334)
From: Optimizing expression quantitative trait locus mapping workflows for single-cell studies
Random effect matrix | Discovery | a-bulk replication | |||||
|---|---|---|---|---|---|---|---|
kinship | 1/#cells | 1/#reads | eGenes | % tested | # replicated | % replicated | |
d-mean | ✓ | – | – | 1415 | 6.96% | 1086 | 76.75% |
d-mean | – | ✓ | – | 1652 | 8.12% | 1251 | 75.73% |
d-mean | – | – | ✓ | 1645 | 8.09% | 1233 | 74.95% |
dr-mean | ✓ | – | – | 2073 | 10.19% | 1466 | 70.72% |
dr-mean | ✓ | ✓ | – | 2750 | 13.52% | 1832 | 66.62% |
dr-mean | ✓ | – | ✓ | 2458 | 12.09% | 1676 | 68.19% |