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| PIGE-package | Gene and pathway p-values using the Adaptive Rank Truncated Product test |
| ARTP.GE | Gene and pathway p-values using ARTP method |
| bootstrap.snp | Parallel computing of the Likelihhod ratio test (or Wald test) for an interaction term (or a simple SNP effect) on bootstrap sample |
| compute.p.snp.obs | Likelihhod ratio test (or Wald test) for an interaction term (or a single SNP effect) |
| data.pathway | Fictive data frame corresponding to the gene x pathway analysis for the example of case-control study. |
| data.pathway.surv | Fictive data frame corresponding to the gene x pathway analysis for the example of survival analysis. |
| data.pige | Sample data of a case-control study |
| data.surv | Fictive data set for sample data of a survival analysis. |
| data.to.list.gene.snp | Annotation gene/SNP |
| data.to.PIGE | Generate data for Gene- and Pathway-environment interaction |
| list.gene.snp | Fictive list for the case-control study example containing the names of the snp for each gene included in the studied pathways |
| list.gene.snp.surv | Fictive list (for survival example) containing the names of the snp for each gene included in the studied pathways |
| LR.cont | Wald test for an adjusted model. |
| LR.cont.boot | Wald test for an adjusted model. |
| LR.cont.surv | Wald test for an adjusted model. |
| LR.inter.cat | Likelihhod ratio test for an interaction term |
| LR.inter.cat.boot | Likelihhod ratio test for an interaction term |
| LR.inter.cat.surv | Likelihhod ratio test for an interaction term |
| LR.inter.cont | Wald test for an interaction term |
| LR.inter.cont.boot | Wald test for an interaction term |
| LR.inter.cont.surv | Wald test for an interaction term |
| permutation.snp | Parallel computing of the Likelihhod ratio test (or Wald test) for an interaction term (or a simple SNP effect) on permutation sample |
| PIGE | Gene and pathway p-values using the Adaptive Rank Truncated Product test |
| snp.gene.select | Fictive data frame containing the names of the gene (first column) and the names of the SNP belonging to the SNPS (second column) |