Tools for Testing Gene-Gene Interaction at the Gene Level

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Documentation for package ‘GeneGeneInteR’ version 1.31.0

• 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