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{| width="1500" border="1" align="left" cellpadding="1" cellspacing="1"
{| width="1500" border="1" align="left" cellpadding="1" cellspacing="1"
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! scope="col" | Association Analysis
! scope="col" |
! scope="col" | Statistical Test
Association Analysis
! scope="col" | Subset of SNPs
! scope="col" | Output File Type
! scope="col" |
! scope="col" | Output Filename Format
Statistical Test
! scope="col" |
Subset of SNPs
! scope="col" |
Output File Type
! scope="col" |
Output Filename Format
|-
|-
| A. Typical DIAGRAM analysis using existing association pipeline
|
| Wald or likelihood ratio
A. Typical DIAGRAM analysis using existing association pipeline
| All SNPs with min MAC >= 1
| Custom file based on DIAGRAM format
|
| DIAGRAMv4_QQQ_XXX_1000G_KKK_YYY_ZZZ.txt
Wald or likelihood ratio
|
All SNPs with min MAC >= 1
|
Custom file based on DIAGRAM format
|
DIAGRAMv4_QQQ_XXX_1000G_KKK_YYY_ZZZ.txt
|-
|-
| B. Analysis of all SNPs using logistic regression score test
|
| Score test
B. Analysis of all SNPs using logistic regression score test
| All SNPs with min MAC >= 1
| EPACTS output file
|
| DIAGRAMv4_QQQ_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts
Score test
|
All SNPs with min MAC >= 1
|
EPACTS output file
|
DIAGRAMv4_QQQ_XXX_1000G_KKK_SCR_YYY_ZZZ.epacts
|-
|-
| C. Analysis of low frequency variants using Firth bias-corrected logistic regression
|
| Firth bias-corrected
C. Analysis of low frequency variants using Firth bias-corrected logistic regression
| SNPs with 200 >= MAC >= 1
| EPACTS output file
|
| DIAGRAMv4_QQQ_XXX_1000G_KKK_FIR_YYY_ZZZ.epacts
Firth bias-corrected
|
SNPs with 200 >= MAC >= 1
|
EPACTS output file
|
DIAGRAMv4_QQQ_XXX_1000G_KKK_FIR_YYY_ZZZ.epacts
|}
|}
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