PIGE: Self contained gene set analysis for gene- and pathway-environment interaction analysis
Version 0.9

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

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PIGE")

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...

Functions

ARTP.GE Man page Source code
LR.cont Man page Source code
LR.cont.surv Man page Source code
LR.inter.cat Man page Source code
LR.inter.cat.surv Man page Source code
LR.inter.cont Man page Source code
LR.inter.cont.surv Man page Source code
PIGE Man page
PIGE-package Man page
compute.p.snp.obs Man page Source code
data.pathway Man page
data.pathway.surv Man page
data.pige Man page
data.surv Man page
data.to.PIGE Man page Source code
data.to.list.gene.snp Man page Source code
list.gene.snp Man page
list.gene.snp.surv Man page
permutation.snp Man page Source code
permutation.wrapper.cat.inter Man page Source code
permutation.wrapper.cat.inter.Y.and.X Man page Source code
permutation.wrapper.cont Man page Source code
permutation.wrapper.cont.Y.and.X Man page Source code
permutation.wrapper.cont.inter Man page Source code
permutation.wrapper.cont.inter.Y.and.X Man page Source code
snp.gene.select Man page

Files

inst
inst/sampleData
inst/sampleData/res-permut-surv.txt
inst/sampleData/res-permut.txt
inst/sampleData/res-obs-surv.txt
inst/sampleData/snp.gene.surv.txt
inst/sampleData/SNP-GENE-annotation.txt
inst/sampleData/res-obs.txt
NAMESPACE
data
data/data.pathway.rda
data/data.pathway.surv.rda
data/data.pige.rda
data/snp.gene.select.rda
data/data.surv.rda
data/list.gene.snp.rda
data/list.gene.snp.surv.rda
R
R/permutation.wrapper.cont.inter.Y.and.X.R
R/LR.inter.cat.R
R/LR.inter.cat.surv.R
R/permutation.wrapper.cat.inter.R
R/data.to.PIGE.R
R/PIGE-package.R
R/LR.cont.surv.R
R/permutation.wrapper.cat.inter.Y.and.X.R
R/LR.inter.cont.R
R/data.to.list.gene.snp.R
R/compute.p.snp.obs.R
R/LR.inter.cont.surv.R
R/permutation.wrapper.cont.inter.R
R/ARTP-GE.R
R/LR.cont.R
R/permutation.wrapper.cont.Y.and.X.R
R/permutation.snp.R
R/permutation.wrapper.cont.R
MD5
DESCRIPTION
man
man/permutation.snp.Rd
man/LR.cont.Rd
man/list.gene.snp.surv.Rd
man/permutation.wrapper.cat.inter.Y.and.X.Rd
man/LR.inter.cat.surv.Rd
man/data.to.list.gene.snp.Rd
man/permutation.wrapper.cont.inter.Rd
man/permutation.wrapper.cont.inter.Y.and.X.Rd
man/LR.cont.surv.Rd
man/permutation.wrapper.cont.Rd
man/snp.gene.select.Rd
man/permutation.wrapper.cont.Y.and.X.Rd
man/data.pige.Rd
man/data.to.PIGE.Rd
man/PIGE-package.Rd
man/compute.p.snp.obs.Rd
man/LR.inter.cat.Rd
man/LR.inter.cont.surv.Rd
man/LR.inter.cont.Rd
man/data.pathway.Rd
man/permutation.wrapper.cat.inter.Rd
man/data.surv.Rd
man/data.pathway.surv.Rd
man/list.gene.snp.Rd
man/ARTP.GE.Rd
PIGE documentation built on May 19, 2017, 10:24 p.m.