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<pre>epacts2.1/epacts single -man
<pre>epacts2.1/epacts single -man
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<br> To simplify the reporting process, '''only analyze the imputed SNPs. '''
<br> To simplify the reporting process, '''only analyze the imputed SNPs. '''
=== Primary analyses ===
=== Primary analyses ===
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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline 1. Typical DIAGRAM analysis using existing association pipeline]
[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline 1. Typical DIAGRAM analysis using existing association pipeline] (with or without BMI)
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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#C._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression 2. Analysis of low frequency variants using Firth bias-corrected logistic regression]
[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#C._Analysis_of_low_frequency_variants_using_Firth_bias-corrected_logistic_regression 2. Analysis of low frequency variants using Firth bias-corrected logistic regression] (with or without BMI)
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For quality control, please run an additional analysis using EPACTS on all SNPs for chromosome 20 only using the '''SCORE''' test without BMI adjustment. These results will be used to compare with results from the primary analyses, to ensure the new EPACTS software has been run correctly.
For quality control, please run an additional analysis using EPACTS on all SNPs for chromosome 20 only using the '''SCORE''' test without BMI adjustment. These results will be used to compare with results from the primary analyses, to ensure the new EPACTS software has been run correctly.
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{| width="1650" border="1" cellpadding="1" cellspacing="1" align="center"
{| width="1650" border="1" cellpadding="1" cellspacing="1" align="center"
| align="center" | '''Output Filename Format'''
| align="center" | '''Output Filename Format'''
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| [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#3._Analysis_of_chromosome_20_using_logistic_regression_score_test 3. Analysis of chromosome 20 using logistic regression score test]
| [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#3._Analysis_of_chromosome_20_using_logistic_regression_score_test 3. Analysis of chromosome 20 using logistic regression score test] (without BMI)
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| Score test
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*FBC = Firth Bias Corrected Logistic Regression
*FBC = Firth Bias Corrected Logistic Regression
'''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our European colleagues)<br>'''ZZZ '''indicates the name + other initials of the uploader (e.g., BFV, LJS, ABC, etc.)
'''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our European colleagues)<br>'''ZZZ '''indicates the name + other initials of the uploader (e.g., BFV, LJS, ABC, etc.)
=== 1. Typical DIAGRAM analysis using existing association pipeline<br> ===
=== 1. Typical DIAGRAM analysis using existing association pipeline<br> ===
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=== 3. Analysis of chromosome 20 using logistic regression score test ===
The score test has well-controlled type I error rate and good power for meta-analysis of balanced (equal numbers of cases and controls) studies. It is also very computationally efficient. Please run the score test using the EPACTS software.
The score test has well-controlled type I error rate and good power for meta-analysis of balanced (equal numbers of cases and controls) studies. It is also very computationally efficient. Please run the score test using the EPACTS software.
The EPACTS command for the score test analysis of chromosome 20 is:
The EPACTS command for the score test analysis of chromosome 20 is:
