Table 2. Performances of Each Method When Only a Single Time Point Is Truly Associated with Y (Scenario 2)a.
| performance
to identify the true exposures independently
of the true time point (s) |
performance
to identify the true exposures
at the true time point (s) |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sensitivity |
FDR |
sensitivity |
FDR |
|||||||||
| N true predictors | 3 | 5 | 10 | 3 | 5 | 10 | 3 | 5 | 10 | 3 | 5 | 10 |
| Raw Data (1-Step) | ||||||||||||
| ExWAS.none | 99 (5.7) | 93.8 (10.5) | 78.5 (11.8) | 87.9 (3.1) | 82.4 (4.1) | 73.4 (6.1) | 99 (5.7) | 92 (11.7) | 72.5 (14) | 93.5 (1.9) | 90.3 (3.4) | 87 (4) |
| ExWAS.bon | 75.7 (24.1) | 39.4 (20.2) | 16 (13.1) | 15 (22.3) | 14.6 (22.5) | 20.9 (28.3) | 74 (24.9) | 38.4 (20) | 15.1 (12.6) | 42 (30.4) | 34.1 (31.8) | 34.1 (33.8) |
| ExWAS.by | 69.7 (29.2) | 35.2 (23.6) | 11.8 (14.7) | 12.5 (20.7) | 12.6 (22.7) | 16.6 (26.2) | 69 (29.3) | 34.8 (23.5) | 11.5 (14.4) | 35.7 (33.3) | 28.7 (33.3) | 24.1 (32.4) |
| ExWAS-MLR.none | 68.7 (28) | 51 (19.8) | 25.4 (13.8) | 70.3 (14.7) | 66.3 (14) | 64.4 (15.5) | 66.3 (27.4) | 47.6 (20.1) | 20.7 (13.9) | 71.9 (14.5) | 69.4 (13.9) | 72.6 (15.9) |
| ExWAS-MLR.bon | 63 (28) | 29.6 (19) | 11.1 (11.9) | 8.2 (22.7) | 5.7 (14.8) | 14.7 (30.1) | 60.7 (28.2) | 28 (18.9) | 10.2 (11.1) | 14 (26.4) | 10.5 (21.8) | 18.9 (32.2) |
| ExWAS-MLR.by | 58 (30.2) | 27.4 (19.6) | 7.7 (10.8) | 6.2 (20) | 7.5 (20) | 11.2 (24.8) | 56 (29.9) | 26 (19.4) | 7.2 (10.3) | 10.4 (24.1) | 11.2 (25.2) | 12.9 (27.3) |
| ENET | 36 (34.7) | 15.2 (23.8) | 5.5 (11.8) | 2.5 (10.3) | 4.1 (15.2) | 8.2 (25) | 33.7 (33.3) | 13 (20.4) | 4.9 (10.7) | 7.2 (18.9) | 9.3 (22.9) | 12.2 (30.5) |
| sPLS | 84.3 (22.4) | 58.2 (26.2) | 28.8 (23.6) | 17.3 (22.9) | 23 (25.3) | 28.8 (30.7) | 78.3 (24.8) | 54.2 (26.1) | 25.6 (22.5) | 29 (29.8) | 35.5 (30) | 43.4 (34.9) |
| DSA | 78.3 (27) | 45.6 (27.3) | 15.1 (15.1) | 13.5 (20.6) | 14.8 (21.8) | 14.3 (26.6) | 70.7 (27.7) | 39.6 (24.9) | 12.2 (12.4) | 21.5 (24.4) | 22.3 (27.6) | 23 (32.5) |
| sNPLS | 72 (23.6) | 54.4 (27.6) | 42.5 (29.3) | 32.4 (32) | 43.8 (33.5) | 46.6 (29.8) | 71 (23.5) | 52.4 (28.3) | 40.4 (29.8) | 53.7 (33.1) | 65.7 (27) | 60.6 (31.7) |
| DLNM | 53 (29.3) | 25 (20.2) | 6.7 (9.2) | 14 (23.7) | 14.3 (26.3) | 24.7 (38.7) | 43.3 (26.6) | 19.2 (16.3) | 4.7 (7.2) | 54.1 (31.7) | 49.4 (35.8) | 48.4 (43.2) |
| Averaged Data (2-Step) | ||||||||||||
| ExWAS.none | 89 (15.7) | 73.6 (21.6) | 51.2 (15.5) | 74.1 (10.2) | 66.7 (15.2) | 60.2 (14.6) | 89 (15.7) | 72.6 (22) | 49.4 (15.9) | 90.7 (4) | 87.8 (6) | 86.3 (5.8) |
| ExWAS.bon | 52.3 (27.3) | 23.8 (20.4) | 11.4 (12.1) | 14.7 (24.2) | 12.9 (24.5) | 24.3 (32.9) | 52.3 (27.3) | 23.6 (20.2) | 11.3 (12) | 65.5 (27.4) | 53.2 (37.2) | 55 (38.5) |
| ExWAS.by | 43.3 (32.3) | 21.2 (23.4) | 8.2 (12.8) | 11.8 (23.3) | 11.6 (24.4) | 13 (24.9) | 43.3 (32.3) | 21.2 (23.4) | 8.2 (12.8) | 60.5 (35.5) | 47.3 (40.8) | 33.5 (41.6) |
| ExWAS-MLR.none | 49 (29) | 31.6 (20.9) | 12.1 (9.5) | 32 (30.7) | 31.5 (32.4) | 30.7 (37.3) | 46.3 (27.6) | 28.6 (21.1) | 9.7 (8.2) | 39.2 (31.2) | 42.5 (33.9) | 43.6 (38.6) |
| ExWAS-MLR.bon | 39 (26.8) | 14.2 (14.6) | 5.6 (6.7) | 5 (19.5) | 4.3 (17.3) | 7.5 (24) | 35.7 (26.5) | 12.4 (13.9) | 4.7 (6.1) | 14.3 (29.7) | 13.8 (30.2) | 14.3 (31.9) |
| ExWAS-MLR.by | 32 (29.2) | 12.6 (15.2) | 3.3 (5.7) | 2.5 (14.9) | 3.7 (16.8) | 3 (13.9) | 29 (27.9) | 10.4 (13.8) | 2.7 (5.1) | 10.8 (26.7) | 13.8 (30.7) | 7.5 (24) |
| ENET | 11 (22.7) | 2.6 (10.1) | 1.4 (5.9) | 2.8 (15) | 1.3 (10.5) | 0.7 (5.3) | 10.3 (22.1) | 1.2 (5.6) | 1.2 (5) | 4.6 (19.3) | 6.3 (23.5) | 1.8 (11.6) |
| sPLS | 63.7 (29.6) | 42.8 (28.7) | 29 (23.3) | 22.1 (28.4) | 28.8 (31.2) | 28.9 (32.3) | 60 (31.1) | 39.8 (28.4) | 26.8 (23.9) | 49.1 (36) | 56.9 (33.8) | 59.1 (36.5) |
| DSA | 59.7 (29.3) | 27.6 (26.8) | 13 (14) | 13.6 (23.1) | 19.6 (30.6) | 18 (28.5) | 53.3 (29.6) | 21.6 (23) | 10.1 (11.3) | 34.9 (33.2) | 43.9 (37.8) | 35.6 (35.7) |
a
Abbreviations: DSA, deletion-substitution-addition algorithm; ExWAS, exposome-wide association study; ENET, elastic net; FDR, false discovery rate; MLR, multiple linear regression; sPLS, sparse partial least-squares.