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, 17:09, 11 October 2012
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| <pre>epacts2.1/epacts single -man | | <pre>epacts2.1/epacts single -man |
| </pre> | | </pre> |
− | To simplify the reporting process, o | + | To simplify the reporting process, o |
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− | There are '''4''' separate association analyses to be completed (score and Firth, with and without adjustment for BMI): | + | There are '''4''' separate association analyses to be completed (sco |
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− | {| width="1500" border="1" align="left" cellpadding="1" cellspacing="1" | + | {| width="1600" border="1" align="left" cellpadding="1" cellspacing="1" |
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| ! scope="col" | | | ! scope="col" | |
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− | DIAGRAMv4_iSNPs_XXX_1000G_KKK_TTT_YYY_ZZZ.txt | + | A. DIAGRAMv4_iSNPs_XXX_1000G_KKK_TTT_YYY_ZZZ.txt |
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− | DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_TTT_YYY_ZZZ.txt | + | B. DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_TTT_YYY_ZZZ.txt |
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− | SNPs with | + | SNPs with |
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| 200 >= MAC >= 1 | | 200 >= MAC >= 1 |
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− | DIAGRAMv4_iSNPs_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts | + | A. DIAGRAMv4_iSNPs_XXX_1000G_KKK_FBC_YYY_ZZZ.epacts |
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− | DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_FBC_YYY_ZZZ.epacts | + | B. DIAGRAMv4_iSNPs_XXX_adjBMI_1000G_KKK_FBC_YYY_ZZZ.epacts |
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| |} | | |} |
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− | </pre> | + | </pre> |
| 3. Analysis of all SNPs using logistic regression score test<br>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. | | 3. Analysis of all SNPs using logistic regression score test<br>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. |
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− | The EPACTS command for the score test analysis of all variants is: | + | The EPACTS command for the score test analysis of all variants is: |
| <pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \ | | <pre>epacts2.1/epacts single -vcf [INPUT VCF FILENAME] -ped [INPUT PED FILENAME] -out [OUTPUT FILENAME PREFIX] \ |
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− | </pre> | + | </pre> |
| This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. Add the relevant additional covariates with additional "-cov" options. This assumes that the VCF files are separated by chromosomes (option -sepchr). All variants with at least one minor allele count will be analyzed (option -min-mac 1). It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10). | | This command will run single variant analysis using the score test logistic regression on the DISEASE phenotype adjusting for AGE. Add the relevant additional covariates with additional "-cov" options. This assumes that the VCF files are separated by chromosomes (option -sepchr). All variants with at least one minor allele count will be analyzed (option -min-mac 1). It will annotate results by functional category (option -anno) and run the analysis on 10 parallel CPUs (option -run 10). |
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