Genome-wide association/interaction analyses with family data


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Documentation for package ‘GWAF’ version 2.0

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GWAF-package Genome-wide association/interaction analyses with family data
%*%-method Class "bdsmatrix"
%*%-method Class "gchol.bdsmatrix"
all-method Class "bdsmatrix"
any-method Class "bdsmatrix"
auto function to generate scripts for genome-wide association/interaction analysis
bdsmatrix-class Class "bdsmatrix"
coerce-method Class "bdsmatrix"
coerce-method Class "gchol"
coerce-method Class "gchol.bdsmatrix"
diag-method Class "bdsmatrix"
diag-method Class "gchol"
diag-method Class "gchol.bdsmatrix"
diag<--method Class "bdsmatrix"
dim-method Class "bdsmatrix"
dim-method Class "gchol.bdsmatrix"
dimnames-method Class "bdsmatrix"
dimnames<--method Class "bdsmatrix"
gchol Generalized Cholesky decompostion
gchol-class Class "gchol"
gchol-method Methods for Function gchol in Package 'kinship'
gchol-methods Methods for Function gchol in Package 'kinship'
gchol.bdsmatrix Generalized Cholesky decompostion
gchol.bdsmatrix-class Class "gchol.bdsmatrix"
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 association 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 association 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 interaction 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 interaction 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 interaction 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 interaction between a continuous trait and a batch of imputed SNPs in families using Generalized Estimation Equation model
GWAF Genome-wide association/interaction analyses with family data
GWplot function for making genome-wide p-value plot
lmekin function for linear mixed effects modeling with a kinship coefficient matrix
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 interaction 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
makekinship Create a kinship matrix
Math-method Class "bdsmatrix"
Math2-method Class "bdsmatrix"
max-method Class "bdsmatrix"
min-method Class "bdsmatrix"
Ops-method Class "bdsmatrix"
prod-method Class "bdsmatrix"
qq function to make Qantile-Qantile (QQ) plot for p-values
range-method Class "bdsmatrix"
show-method Class "bdsmatrix"
show-method Class "gchol"
show-method Class "gchol.bdsmatrix"
sum-method Class "bdsmatrix"
unique-method Class "bdsmatrix"
[-method Class "bdsmatrix"
[-method Class "gchol.bdsmatrix"