Genome-Wide Association/Interaction Analysis and Rare Variant Analysis with Family Data

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Documentation for package ‘GWAF’ version 2.2

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GWAF-package Genome-wide association/interaction analysis and rare variant analysis with family data
auto function to generate scripts for genome-wide association/interaction analysis
geepack.lgst function for testing association between a dichotomous trait and a genotyped SNP in family data using Generalized Estimation Equation model
geepack.lgst.batch function to test genetic associations between a dichotomous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
geepack.lgst.batch.imputed function to test genetic associations between a dichotomous trait and a batch of imputed SNPs in families using Generalized Estimation Equation model
geepack.lgst.imputed function for testing association between a dichotomous trait and an imputed SNP in family data using Generalized Estimation Equation model
geepack.lgst.int function for testing gene-environment or gene-gene interaction between a dichotomous trait and a genotyped SNP in family data using Generalized Estimation Equation model
geepack.lgst.int.batch function to test gene-environment or gene-gene interactions between a dichotomous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
geepack.lgst.int.batch.imputed function to test gene-environment or gene-gene interactions between a dichotomous trait and a batch of imputed SNPs in families using Generalized Estimation Equation model
geepack.lgst.int.imputed function for testing gene-environment or gene-gene interaction between a dichotomous trait and an imputed SNP in family data using Generalized Estimation Equation model
geepack.quant.batch function to test genetic associations between a continuous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
geepack.quant.batch.imputed function to test associations between a continuous trait and a batch of imputed SNPs in families using Generalized Estimation Equation model
geepack.quant.int.batch function to test gene-environment or gene-gene interactions for a continuous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
geepack.quant.int.batch.imputed function to test gene-environment or gene-gene interactions between a continuous trait and a batch of imputed SNPs in families using Generalized Estimation Equation model
glmm.lgst function for testing association between a dichotomous trait and a genotyped SNP in family data using Generalized Linear Mixed Effects model
glmm.lgst.batch function to test genetic association between a dichotomous trait and a batch of genotyped SNPs in families using Generalized Linear Mixed Effects model
GWAF Genome-wide association/interaction analysis and rare variant analysis with family data
GWplot function for making genome-wide p-value plot
lmepack.batch function to test genetic associations between a continuous trait and a batch of genotyped SNPs in families using Linear Mixed Effects model
lmepack.batch.imputed function to test associations between a continuous trait and a batch of imputed SNPs in families using Linear Mixed Effects model
lmepack.int.batch function to test gene-environment or gene-gene interactions for a continuous trait and a batch of genotyped SNPs in families using Linear Mixed Effects model
lmepack.int.batch.imputed function to test gene-environment or gene-gen interaction and associations between a continuous trait and a batch of imputed SNPs in families using Linear Mixed Effects model
lmeVpack.batch.imputed function to efficiently test associations between a continuous trait and a batch of imputed SNPs in families using Linear Mixed Effects model
qq function to make Qantile-Qantile (QQ) plot for p-values