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GWAF (version 2.2)

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

Description

Functions for genome-wide association/interaction analysis and rare variant analysis on a continuous/dichotomous trait using family data, and for making genome-wide p-value plot and QQ plot.

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Version

Install

install.packages('GWAF')

Monthly Downloads

42

Version

2.2

License

GPL (>= 2)

Maintainer

Ming-Huei Chen

Last Published

March 12th, 2015

Functions in GWAF (2.2)

GWplot

function for making genome-wide p-value plot
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
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
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
GWAF-package

Genome-wide association/interaction analysis and rare variant analysis with family data
qq

function to make Qantile-Qantile (QQ) plot for p-values
geepack.lgst

function for testing association between a dichotomous trait and a genotyped SNP in family data 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
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.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.batch

function to test genetic association between a dichotomous trait and a batch of genotyped SNPs in families using Generalized Linear Mixed Effects model
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
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.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.imputed

function for testing association between a dichotomous trait and an imputed SNP in family data 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
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
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.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.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.quant.batch

function to test genetic associations between a continuous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
auto

function to generate scripts for genome-wide association/interaction analysis