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Table 3 Robustness of the proposed correction

From: A correction for sample overlap in genome-wide association studies in a polygenic pleiotropy-informed framework

True correlation

Plug-in correlation

TP

FP

FDP

0.4

0.3

261.16 (260.27, 262.85)

2.42 (2.12, 2.71)

0.0091 (0.0080, 0.0102)

0.4

0.35

252.20 (250.92, 253.48)

1.56 (1.32, 1.80)

0.0061 (0.0052, 0.0070)

0.4

0.375

247.78 (246.79, 249.06)

1.48 (1.22, 1.73)

0.0059 (0.0049, 0.0069)

0.4

0.4

243.59 (242.31, 244.879)

1.40 (1.17, 1.63)

0.0057 (0.0048, 0.0066)

0.4

0.425

238.72 (237.42, 240.02)

1.60 (1.38, 1.82)

0.0066 (0.0057, 0.0075)

0.4

0.45

235.11 (233.88, 236.34)

1.96 (1.72, 2.20)

0.0082 (0.0072, 0.0092)

0.4

0.5

234.81 (233.57, 236.04)

1.96 (1.72, 2.20)

0.0082 (0.0072, 0.0092)

  1. For the “positive pleiotropy A” scenario the correlation due to overlap is 0.4. Here we varied the correlation value in the de-correlation step from 0.3 to 0.5. TP, true positives; FP false positives, FDP, false discovery proportion