# PedGenie Description of FunctionalityΒΆ

PedGenie is now part of our new Genie package. It functions 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-based Hardy-Weinburg Equilibrium

Allele-based Hardy-Weinburg Equilibrium

Genotype-based Q test for Odds Ratio

**Quantitative Outcome**

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]

Detailed description of .rgen XML file

All PedGenie Example Files