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Validate association p values at typed SNPs | options | |||||||||||||||||
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1) Validate p values for genetic association by haplotype reference data in VCF format or PLINK format |
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| Hint: If the reference genotypes are stored in different files chromosome by chromosome, you can use _CHROM_ to denote the chromosome names [1...Y] in the file name. e.g. chr_CHROM_.phase1.cvf.chinese. |
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| Output: | |||||||||
| Description | |
| .... | |
| ImputePValue | The imputed p-value |
| Confidence | The (1-variance) of the conditional normal distribution on which the imputation was carried out. It ranges from 0 to 1. The larger the better. The cut-off 0.4 is recommended. |
| ProbC | The probability of the observed p-value is equal to the imputed p-value. In principle, it is measured by by Prob(Z>=the corresponding z score of the observed p-value ) if the z score is over the mean of the conditional normal distribution; otherwise 1-Prob(Z>=the corresponding z score of the observed p-value ). The smaller ProbC the less likely the observed p-value is supported by its nearby SNPs in high LD. For whole genome data, the cutoff ProbC, 1E-6 is recommended. Note when the confidence score is low say < 0.6, the ProbC will be not calculated. A '.' will appear. |
Miao-xin Li, Jia-en Deng, Center for Genomic Sciences & Department of Psychiatry, The University of Hong Kong, All rights reserved.