Table 2 |
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|
Type I error estimate at alpha = 0.05 with 10,000 replicates of phenotype and a single SNP in LE with a QTL explaining 10% phenotype variation. |
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|
MAF |
Polygenic Variance |
LM |
LME |
FBAT |
LM-LME 1 |
LM-LME 2 |
|
|
||||||
|
0.005 |
0.3 |
0.087 |
0.046 |
0.052 |
0.044 |
0.045 |
|
0.005 |
0.6 |
0.118 |
0.053 |
0.047 |
0.046 |
0.050 |
|
0.01 |
0.3 |
0.089 |
0.050 |
0.049 |
0.048 |
0.050 |
|
0.01 |
0.6 |
0.122 |
0.049 |
0.048 |
0.044 |
0.048 |
|
0.05 |
0.3 |
0.087 |
0.048 |
0.052 |
0.047 |
0.048 |
|
0.05 |
0.6 |
0.118 |
0.050 |
0.050 |
0.043 |
0.047 |
|
0.1 |
0.3 |
0.082 |
0.044 |
0.053 |
0.041 |
0.043 |
|
0.1 |
0.6 |
0.122 |
0.049 |
0.054 |
0.043 |
0.047 |
|
|
||||||
|
The SNP explains 0% phenotype variation. A QTL is simulated to explain 10% phenotype variation and in LE with the SNP. Marginal phenotype distribution follows the standard normal distribution. LM_LME1: two-stage approach with LM (p-value cut-off 0.1) at first stage LM_LME2: two-stage approach with LM (p-value cut-off 0.2) at first stage |
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|
Chen et al. BMC Genetics 2010 11:40 doi:10.1186/1471-2156-11-40 |
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