PIGE: Self contained gene set analysis for gene- and pathway-environment interaction analysis

Extension of the ARTP package for gene- and pathway-environment interaction

AuthorBenoit Liquet, Therese Truong
Date of publication2013-12-30 07:44:39
MaintainerBenoit Liquet <benoit.liquet@isped.u-bordeaux2.fr>
LicenseGPL (>= 2.0)
Version0.9

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Man pages

ARTP.GE: Gene and pathway p-values using ARTP method

compute.p.snp.obs: Likelihhod ratio test (or Wald test) for an interaction term...

data.pathway: Fictive data frame corresponding to the gene x pathway...

data.pathway.surv: Fictive data frame corresponding to the gene x pathway...

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...

list.gene.snp.surv: Fictive list (for survival example) containing the names of...

LR.cont: 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.surv: Likelihhod ratio test for an interaction term

LR.inter.cont: 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...

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

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

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

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

permutation.wrapper.cont.inter.Y.and.X: Internal function used for the parallel computation on the...

permutation.wrapper.cont.Y.and.X: Internal function used for the parallel computation on the...

PIGE-package: Gene and pathway p-values using the Adaptive Rank Truncated...

snp.gene.select: Fictive data frame containing the names of the gene (first...

Files in this package

PIGE
PIGE/inst
PIGE/inst/sampleData
PIGE/inst/sampleData/res-permut-surv.txt
PIGE/inst/sampleData/res-permut.txt
PIGE/inst/sampleData/res-obs-surv.txt
PIGE/inst/sampleData/snp.gene.surv.txt
PIGE/inst/sampleData/SNP-GENE-annotation.txt
PIGE/inst/sampleData/res-obs.txt
PIGE/NAMESPACE
PIGE/data
PIGE/data/data.pathway.rda
PIGE/data/data.pathway.surv.rda
PIGE/data/data.pige.rda
PIGE/data/snp.gene.select.rda
PIGE/data/data.surv.rda
PIGE/data/list.gene.snp.rda
PIGE/data/list.gene.snp.surv.rda
PIGE/R
PIGE/R/permutation.wrapper.cont.inter.Y.and.X.R PIGE/R/LR.inter.cat.R PIGE/R/LR.inter.cat.surv.R PIGE/R/permutation.wrapper.cat.inter.R PIGE/R/data.to.PIGE.R PIGE/R/PIGE-package.R PIGE/R/LR.cont.surv.R PIGE/R/permutation.wrapper.cat.inter.Y.and.X.R PIGE/R/LR.inter.cont.R PIGE/R/data.to.list.gene.snp.R PIGE/R/compute.p.snp.obs.R PIGE/R/LR.inter.cont.surv.R PIGE/R/permutation.wrapper.cont.inter.R PIGE/R/ARTP-GE.R PIGE/R/LR.cont.R PIGE/R/permutation.wrapper.cont.Y.and.X.R PIGE/R/permutation.snp.R PIGE/R/permutation.wrapper.cont.R
PIGE/MD5
PIGE/DESCRIPTION
PIGE/man
PIGE/man/permutation.snp.Rd PIGE/man/LR.cont.Rd PIGE/man/list.gene.snp.surv.Rd PIGE/man/permutation.wrapper.cat.inter.Y.and.X.Rd PIGE/man/LR.inter.cat.surv.Rd PIGE/man/data.to.list.gene.snp.Rd PIGE/man/permutation.wrapper.cont.inter.Rd PIGE/man/permutation.wrapper.cont.inter.Y.and.X.Rd PIGE/man/LR.cont.surv.Rd PIGE/man/permutation.wrapper.cont.Rd PIGE/man/snp.gene.select.Rd PIGE/man/permutation.wrapper.cont.Y.and.X.Rd PIGE/man/data.pige.Rd PIGE/man/data.to.PIGE.Rd PIGE/man/PIGE-package.Rd PIGE/man/compute.p.snp.obs.Rd PIGE/man/LR.inter.cat.Rd PIGE/man/LR.inter.cont.surv.Rd PIGE/man/LR.inter.cont.Rd PIGE/man/data.pathway.Rd PIGE/man/permutation.wrapper.cat.inter.Rd PIGE/man/data.surv.Rd PIGE/man/data.pathway.surv.Rd PIGE/man/list.gene.snp.Rd PIGE/man/ARTP.GE.Rd

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