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PIGE (version 1.1)

Self Contained Gene Set Analysis for Gene- And Pathway-Environment Interaction Analysis

Description

Extension of the 'ARTP' package (Yu, K., et al. (2009) ) for gene- and pathway-environment interaction. A permutation and a parametric bootstrap approaches have been implemented for investigating gene- and pathway-environment interaction analysis (Truong, T., et al. (2014) ).

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Version

Install

install.packages('PIGE')

Monthly Downloads

1

Version

1.1

License

GPL (>= 2.0)

Maintainer

Benoit Liquet

Last Published

August 30th, 2017

Functions in PIGE (1.1)

LR.cont.boot

Wald test for an adjusted model.
LR.cont.surv

Wald test for an adjusted model.
LR.inter.cat.surv

Likelihhod ratio test for an interaction term
LR.inter.cont

Wald test for an interaction term
data.pige

Sample data of a case-control study
data.surv

Fictive data set for sample data of a survival analysis.
LR.inter.cont.boot

Wald test for an interaction term
LR.inter.cont.surv

Wald test for an interaction term
bootstrap.wrapper.cat.inter.Y.and.X

Internal function used for the parallel computation on the bootstrap sample
bootstrap.wrapper.cont.Y.and.X

Internal function used for the parallel computation on the bootstrap sample
permutation.wrapper.cat.inter.Y.and.X

Internal function used for the parallel computation on the permutation sample
permutation.wrapper.cat.inter.Y.within.X

Internal function used for the parallel computation on the permutation sample
permutation.wrapper.cont.inter

Internal function used for the parallel computation on the permutation sample
data.to.PIGE

Generate data for Gene- and Pathway-environment interaction
data.to.list.gene.snp

Annotation gene/SNP
PIGE-package

Gene and pathway p-values using the Adaptive Rank Truncated Product test
bootstrap.snp

Parallel computing of the Likelihhod ratio test (or Wald test) for an interaction term (or a simple SNP effect) on bootstrap sample
permutation.wrapper.cont

Internal function used for the parallel computation on the permutation sample
ARTP.GE

Gene and pathway p-values using ARTP method
LR.cont

Wald test for an adjusted model.
data.pathway

Fictive data frame corresponding to the gene x pathway analysis for the example of case-control study.
permutation.wrapper.cont.Y.and.X

Internal function used for the parallel computation on the permutation sample
permutation.wrapper.cont.inter.Y.within.X

Internal function used for the parallel computation on the permutation sample
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)
data.pathway.surv

Fictive data frame corresponding to the gene x pathway analysis for the example of survival analysis.
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.inter.cat

Likelihhod ratio test for an interaction term
LR.inter.cat.boot

Likelihhod ratio test for an interaction term
bootstrap.wrapper.cont.inter.Y.and.X

Internal function used for the parallel computation on the bootstrap sample
compute.p.snp.obs

Likelihhod ratio test (or Wald test) for an interaction term (or a single SNP effect)
permutation.snp

Parallel computing of the Likelihhod ratio test (or Wald test) for an interaction term (or a simple SNP effect) on permutation sample
permutation.wrapper.cont.inter.Y.and.X

Internal function used for the parallel computation on the permutation sample
permutation.wrapper.cat.inter

Internal function used for the parallel computation on the permutation sample