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GWAF (version 2.0)

Genome-wide association/interaction analyses with family data

Description

Functions for genome-wide association analyses and genome-wide interaction analyses 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

2.0

License

GPL (>= 2)

Maintainer

Ming-Huei Chen

Last Published

March 14th, 2013

Functions in GWAF (2.0)

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.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.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
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
GWplot

function for making genome-wide p-value plot
lmepack.batch.imputed

function to test associations between a continuous trait and a batch of imputed SNPs in families using Linear Mixed Effects model
gchol-methods

Methods for Function gchol in Package `kinship'
gchol-class

Class "gchol"
geepack.lgst

function for testing association between a dichotomous trait and a genotyped SNP in family data using Generalized Estimation Equation model
auto

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

Create a kinship matrix
geepack.lgst.imputed

function for testing association between a dichotomous trait and an imputed SNP in family data using Generalized Estimation Equation model
geepack.quant.int.batch.imputed

function to test gene-environment or gene-gene interaction between a continuous trait and a batch of imputed SNPs in families using Generalized Estimation Equation model
qq

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

function to test gene-environment or gene-gene interaction between a dichotomous trait and a batch of imputed SNPs in families using Generalized Estimation Equation 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
geepack.lgst.int.batch

function to test gene-environment or gene-gene interaction between a dichotomous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
geepack.lgst.batch

function to test genetic association between a dichotomous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
bdsmatrix-class

Class "bdsmatrix"
gchol.bdsmatrix-class

Class "gchol.bdsmatrix"
gchol

Generalized Cholesky decompostion
GWAF-package

Genome-wide association/interaction analyses with family data
geepack.lgst.batch.imputed

function to test genetic association between a dichotomous trait and a batch of imputed SNPs in families using Generalized Estimation Equation model
lmekin

function for linear mixed effects modeling with a kinship coefficient matrix
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.int.batch

function to test gene-environment or gene-gene interaction for a continuous trait and a batch of genotyped SNPs in families using Generalized Estimation Equation model
lmepack.int.batch

function to test gene-environment or gene-gene interaction for a continuous trait and a batch of genotyped SNPs in families using Linear Mixed Effects model