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EPACTS for DIAGRAM (view source)

Revision as of 17:29, 11 October 2012

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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. &nbsp;'''
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<br> To simplify the reporting process, '''only analyze the imputed SNPs. &nbsp;'''  
    
=== 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. &nbsp;Typical DIAGRAM analysis using existing association pipeline]&nbsp;(with or without BMI)
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[http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#A._Typical_DIAGRAM_analysis_using_existing_association_pipeline 1. &nbsp;Typical DIAGRAM analysis using existing association pipeline]&nbsp;(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. &nbsp;Analysis of low frequency variants using Firth bias-corrected logistic regression]&nbsp;(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. &nbsp;Analysis of low frequency variants using Firth bias-corrected logistic regression]&nbsp;(with or without BMI)  
    
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=== Analyses for QC  ===
 
=== Analyses for QC  ===
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| 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. &nbsp;Analysis of chromosome 20 using logistic regression score test]&nbsp;(without BMI)
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| [http://genome.sph.umich.edu/wiki/EPACTS_for_DIAGRAM#3._Analysis_of_chromosome_20_using_logistic_regression_score_test 3. &nbsp;Analysis of chromosome 20 using logistic regression score test]&nbsp;(without BMI)  
 
| Score test  
 
| Score test  
 
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'''YYY '''indicates the DATE of file generation (MMDDYY format, e.g. 021710 – apologies in advance to our&nbsp;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&nbsp;European colleagues)<br>'''ZZZ '''indicates the name + other initials of the uploader (e.g., BFV, LJS, ABC, etc.)  
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=== 1. Typical DIAGRAM analysis using existing association pipeline<br>  ===
 
=== 1. Typical DIAGRAM analysis using existing association pipeline<br>  ===
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-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10
 
-test b.firth -pheno DISEASE -cov AGE -sepchr -anno -min-mac 1 -max-mac 200 -run 10
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=== 3. Analysis of chromosome 20 using logistic regression score test  ===
 
=== 3. Analysis of chromosome 20 using logistic regression score test  ===
  
Clement Ma
216

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