PedGenie

PedGenie is now part of our new Genie package. It function as an analysis option of the new package.
Description
When performing an association analysis using family data, one must account for the fact that individuals within a family are related; hence data are correlated. The computed test statistic will be correct; however, the variance will be underestimated and the significance overestimated due to correlations between individuals. PedGenie calculates an empirical p-value for a test statistic using a Monte Carlo approach. Genotypes or haplotypes of individuals within a pedigree are randomly simulated in proportion to a defined allele or haplotype frequency, while still maintaining the original pedigree structure.
Functionality
PedGenie is capable of analyzing dichotomous and quantitative dependent variables. The statistics that PedGenie uses are the standard statistics (as provided by the links on the following websites) as would be used in a sample of independent individuals or independent nuclear families. PedGenie accounts for familial relationships by correcting the significance (p-value) of a statistic through an empirical approach, but leaves the statistic itself unchanged.
The following tests can be performed:
Dichotomous Outcome
Genotype-based Chi-squared test
Allele-based Chi-square test
Genotype-based Chi-square trend test
Genotype-based with Multiple studies CMH Chi-squared test
Genotype-based with Multiple studies CMH Chi-squared trend test
Genotype-based odds ratio
Allele based odds ratio
Genotype-based odds ratio with confidence intervals
Allele based odds ratio with confidence intervals
Genotype-based with Multiple studies meta odds ratio
Genotype-based with Multiple studies meta odds ratio with confidence intervals
Genotype-based with Multiple studies - meta gene-gene 2x2 interactions odds ratio
Genotype-based with Multiple studies - meta gene-gene 2x2 interactions odds ratio with confidence intervals
Trio TDT (Spielman et al 1993)
Sibs TDT (Spielman and Ewens 1998)
Combined Trio/Sibs TDT (Spielman and Ewens 1998)
Genotype-basedHardy-Weinburg Equilibrium
Allele-basedHardy-Weinburg Equilibrium
Genotype-based Q test for Odds Ratio
Quantitative Outcome
Difference in means test
Analysis of Variance (ANOVA)
Quantitative transmission / disequilibrium tests (TDT)
(Allison 1997) (TDT Q5)
(Rabinowitz 1997)
(Monks et al 1998)
How to execute java -jar Genie.jar PedGenie rgenfile[.rgen]
.rgen Parameter File Detailed description of .rgen XML file
PedGenie Examples All PedGenie Example Files

Home   hapMC   hapConstructor