# Tools for Testing Gene-Gene Interaction at the Gene Level

## Documentation for package ‘GeneGeneInteR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

CCA.test | CCA (Canonical-Correlation Analysis) based GGI analysis.
CLD.test | CLD (Composite Linkage Desequilibrium) based GGI analysis.
data.SNP | Multiple genes dataset
gates.test | Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction tests
GBIGM.test | GBIGM (Gene-based information gain method) for GGI analysis.
gene.pair | A case-control dataset with two genes
GGI | Gene-Gene Interaction Analysis of a set of genes
importFile | Imports SNPs information from pedfile, PLINK, VCF (4.0) file, or genotypes imputed by IMPUTE2.
imputeSnpMatrix | Missing values handling for SnpMatrix object
KCCA.test | KCCA (Kernel Canonical-Correlation Analysis) based GGI analysis.
minP.test | Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction tests
PCA.test | PCA-based Gene-Gene Interaction analysis.
plot.GGInetwork | Plot a Gene-Gene Interaction Study with an heatmap-like visualization
PLSPM.test | PLSPM (Partial Least Squares Path Modelling Analysis) based Gene-Gene Interaction analysis.
print.GGItest | Printing objects of class '"GGItest"'
selectSnps | Selects SNPs in snpMatrix and associated info data.frame, outputs of importFile.
snpMatrixScour | SNP filtering based on Minor Allele Frequency, Hardy-Weinberg Equilibrium and call rate
summary.GGInetwork | Printing summaries class '"GGInetwork"' objects
summary.GGItest | Printing summaries class '"GGItest"' objects
tProd.test | Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction tests
tTS.test | Gene-based Gene-Gene Interaction analysis by combining SNP-SNP interaction tests