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) |