![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| 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 |